Glossary

Biochemistry, molecular genetics, and biology glossary terms for Companion Sites.

table index

o-o adhesion signaling tables
o-o cancer tables
o-o cell biology tables
o-o evolution tables
o-o genetics tables
o-o lipids tables
o-o metabolism tables
o-o photosynthesis tables
o-o prokaryote tables

Alphabetic links to Glossary items:
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Companion Sites : Gray Sites α Abiogenesis & EvolutionAlgorithms of Evolution ¤ CancerCell Biology ~ Chemistry of Life Ω Complex Systems ººº CyanobacteriaEnzymesEvo Devo Ơ Fat ф Immunology »» Mechanisms of EvolutionMolecular Biology ** Origin of LifePaleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ SleepStromatolitesTaxonomy Phylogeny ۰۰ Virus • White Sites  Diagrams & Tables æ Eubacteria & Archaea φ MoleculeMolecular Paths ››› PathwaysPhotosynthesis • Black Sites Ǒ Endosymbiosis ō Organics

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adhesion signaling tables

 Cell Adhesion Molecules
 Immune Cytokines
 Receptor Signal Transduction
 Second Messengers
 Cell signaling

adhesion ~ adhesion moleculesapoptosis ~ cadherinscell cyclecell growthcell membranescell motilitycellular fatecellular stress responsecellular survivalchemotaxiscommunicationconcentration gradients ~ cytokinescytoplasmcytoskeletondeath of cellsdeath receptordifferentiation & embryogenesisECMenergy transducersextracellular matrix ~ immunoglobulins ~ integrinsion channelsmicrotubules ¤ mitogensmitosismolecular switchesphysiological function ¤ proliferationprotein degradationpumpsreceptor proteinsreceptor-mediated endocytosis ~ receptor tyrosine kinases ~ Rho GTPaseregulation ~ second messengers ~ selectinstransport

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Companion Sites : Gray Sites α Abiogenesis & EvolutionAlgorithms of Evolution ¤ CancerCell Biology ~ Chemistry of Life Ω Complex Systems ººº CyanobacteriaEnzymesEvo Devo Ơ Fat ф Immunology »» Mechanisms of EvolutionMolecular Biology ** Origin of LifePaleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ SleepStromatolitesTaxonomy Phylogeny ۰۰ Virus • White Sites  Diagrams & Tables æ Eubacteria & Archaea φ MoleculeMolecular Paths ››› PathwaysPhotosynthesis • Black Sites Ǒ Endosymbiosis ō Organics

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cancer tables

 Malignant Transformation
 Oncogenes Proto-oncogenes

¤ Cancer ¤¤ adenoviruses ¤ amplification ¤ carcinogenesis ¤ c-Fos ¤ c-Jun ¤ c-Myc ¤ c-Sis ¤ estrogen receptors ¤ gene amplification ¤ genetic predispositon ¤ HBV ¤ HIV ¤ HPV ¤ HTLV-I ¤ immune evasion ¤ irradiation ¤ malignant transformation ¤ metastasis ¤ mitogens ¤ mutagens ¤ MYC ¤ mutations ¤ neoplasia ¤ neoplastic mutations ¤ non-mutagenic carcinogens ¤ oncogenes ¤ p53 ¤ proliferation ¤ proto-oncogenes ¤ radiation ¤ Ras ¤ Rb ¤ retroviral mechanisms of carcinogenesis ¤ retroviruses ¤ signaling molecules ¤ SRC genes ¤ T-antigens ¤ TP53 ¤ tumor antigens ¤ tumor suppressors ¤ tumorigenic viruses ¤ viral carcinogens ¤ v-Fos ¤ v-Sis ¤ v-Myc ¤

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Companion Sites : Gray Sites α Abiogenesis & EvolutionAlgorithms of Evolution ¤ CancerCell Biology ~ Chemistry of Life Ω Complex Systems ººº CyanobacteriaEnzymesEvo Devo Ơ Fat ф Immunology »» Mechanisms of EvolutionMolecular Biology ** Origin of LifePaleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ SleepStromatolitesTaxonomy Phylogeny ۰۰ Virus • White Sites  Diagrams & Tables æ Eubacteria & Archaea φ MoleculeMolecular Paths ››› PathwaysPhotosynthesis • Black Sites Ǒ Endosymbiosis ō Organics

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cell biology tables

 Apoptosis vs Necrosis
 Apoptosis
 Cell Adhesion Molecules
 Cell signaling
 Immune Cytokines
 Receptor Tyrosine Kinases (RTKs)
 Receptor Signal Transduction
 Second Messengers
 Malignant Transformation
 Oncogenes Proto-oncogenes

CELL BIOLOGYactive transportadhesionapoptosiscell growthcell membranescell motilitycentrioleschemotaxischloroplastchromosomescellular fatecell cyclecell-cycle controlcellular stress responsecentrioleschemotaxischloroplastchromosomesciliacommunicationconcentration gradientscytoplasmcytoskeletondeath of cellsdeath receptordifferentiation & embryogenesisECMenergy transducersendoplasmic reticulumendosomeseukaryotes, eukaryoticexosomeextracellular matrixGolgi apparatusion channelslysosome ¤ malignant transformationmeiosismicrotubulesmigration ¤ mitogensmitosismitochondria, mitochondrionmotility ¤ mutagensnuclear membranenuclear porenucleolusnucleusperoxisomephagocytosisphotosynthesisphysiological functionpinocytosisplant cellprokaryotes, prokaryotic ¤ proliferationprotein degradationproteasome ~ PTKspumpsreceptor proteinsreceptor-mediated endocytosis ~ receptor tyrosine kinasesreproductionribosomes ~ RTKsspindlestructuretimeline of lifetransportvacuolevesicle

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Companion Sites : Gray Sites α Abiogenesis & EvolutionAlgorithms of Evolution ¤ CancerCell Biology ~ Chemistry of Life Ω Complex Systems ººº CyanobacteriaEnzymesEvo Devo Ơ Fat ф Immunology »» Mechanisms of EvolutionMolecular Biology ** Origin of LifePaleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ SleepStromatolitesTaxonomy Phylogeny ۰۰ Virus • White Sites  Diagrams & Tables æ Eubacteria & Archaea φ MoleculeMolecular Paths ››› PathwaysPhotosynthesis • Black Sites Ǒ Endosymbiosis ō Organics

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evolution tables

 Genotype Variability

»» Biological Evolution »» Beyond Darwin and Neo-Darwinism »» Punctuated equilibria »» The modern synthesis »» Basic mechanisms of evolution »» Speciation »» Genetic drift »» Gene flow »» Mutation »» Natural selection »» Horizontal Gene Transfer »» Conjugation »» Transduction »» Transformation »» Non-disjunction »» Genetics : Molecular Genetics »» Important features of the genome and proteome »» Conserved & Consensus »» Deletion »» Duplication »» Frameshift »» Insertion »» Inversion »» Meiosis »» mispairing »» Recombination »» Substitution »» Translocation »» Population Genetics : Population Genetics and Formulae »» Mendel's Laws »» Epistasis »» Bottleneck »» Founder effect »» Persistence of functional gene duplicates »» Phyletic gradualism »» Diagrams & Tables: Biological variation »»

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Companion Sites : Gray Sites α Abiogenesis & EvolutionAlgorithms of Evolution ¤ CancerCell Biology ~ Chemistry of Life Ω Complex Systems ººº CyanobacteriaEnzymesEvo Devo Ơ Fat ф Immunology »» Mechanisms of EvolutionMolecular Biology ** Origin of LifePaleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ SleepStromatolitesTaxonomy Phylogeny ۰۰ Virus • White Sites  Diagrams & Tables æ Eubacteria & Archaea φ MoleculeMolecular Paths ››› PathwaysPhotosynthesis • Black Sites Ǒ Endosymbiosis ō Organics

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genetics tables

 Gene Regulation in E.coli
 Biological variation
 Regulatory Proteins Sequences

Alphabetic links to Glossary items:
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Companion Sites : Gray Sites α Abiogenesis & EvolutionAlgorithms of Evolution ¤ CancerCell Biology ~ Chemistry of Life Ω Complex Systems ººº CyanobacteriaEnzymesEvo Devo Ơ Fat ф Immunology »» Mechanisms of EvolutionMolecular Biology ** Origin of LifePaleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ SleepStromatolitesTaxonomy Phylogeny ۰۰ Virus • White Sites  Diagrams & Tables æ Eubacteria & Archaea φ MoleculeMolecular Paths ››› PathwaysPhotosynthesis • Black Sites Ǒ Endosymbiosis ō Organics

| 0 Guide-Glossary

lipids tables

 lipoproteins
 saturation of triacylglygerols

cell membraneschloroplast ~ diacylglycerolendosomesexosome φ lipids & fatty acidslysosomemitochondrianuclear membranenuclear porenucleolusnucleusperoxisomephagocytosisphospholipases ~ phospholipase C-gamma ~ phospolipidpinocytosis φ sphingolipidsstructure φ triacylglycerolsvacuolevesicle

Alphabetic links to Glossary items:
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Companion Sites : Gray Sites α Abiogenesis & EvolutionAlgorithms of Evolution ¤ CancerCell Biology ~ Chemistry of Life Ω Complex Systems ººº CyanobacteriaEnzymesEvo Devo Ơ Fat ф Immunology »» Mechanisms of EvolutionMolecular Biology ** Origin of LifePaleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ SleepStromatolitesTaxonomy Phylogeny ۰۰ Virus • White Sites  Diagrams & Tables æ Eubacteria & Archaea φ MoleculeMolecular Paths ››› PathwaysPhotosynthesis • Black Sites Ǒ Endosymbiosis ō Organics

| 0 Guide-Glossary

metabolism tables

 Electron Transport Chain vs Oxidative Phosphorylation
 Enzymes Function Krebs Cycle
 Enzymes Cofactors of Krebs Cycle
 Phosphate-handling enzymes

anabolic pathways : • anabolism and catabolismacetyl CoA pathwayCalvin cycleC-3C-4CAM •: Crassulacean Acid Metabolism : Hatch-Slack pathwayelectron transfer chain : redox reactionsHMG-CoA-reductase pathway : Isoprenoid biosynthesis in plants methylerythritol phosphate & HMG-CoA-reductase pathwayLight-reactions •: MEP pathway : mevalonate pathway : mevalonate-dependent (MAD) route : MVA independentPhotosynthesis Overview •: cyclic photophosphorylation :• Light-reactions •: noncyclic photophosphorylation :• Nonoxygenic photosynthesisOxygenic photosynthesisPhotophosphorylation •: cyclic photophosphorylation : noncyclic photophosphorylation :• Nonoxygenic photosynthesisOxygenic photosynthesis : redox reactions : electron transfer chain :

catabolic pathways: acetyl-CoA : aerobic respirationanabolism and catabolismanaplerotic reactionsbeta-oxidationglycolysisglyoxylate cycle : catabolism and anabolismcatabolism : citric acid cycleKrebs cycleoxidative phosporylation : respiration - aerobic • : TCA cycle : tricarboxylic acid cycle • : image catabolism vs anabolism :

Prokaryote metabolism: Carbon fixation in Cyanobacteria, prochlorophytes: • Calvin cycle = C-3 = RuBP • Metabolism • glyoxylate cycle3-hydroxypropionate cyclerACAreductive acetyl CoA pathwayreverse tricarboxyclic acid cyclerTCARuBPProkaryote Physiology & CommunicationInteractions in BacteriaBacterial motilityPhosphorylation switchesPhotosynthetic bacteriaProkaryote Genetics & BiochemistryControl of gene expressionRecombinant DNA Restriction Enzmes Restriction EndonucleasesHorizontal Gene TransferConjugationTransductionTransformationSymbiosis

Alphabetic links to Glossary items:
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Companion Sites : Gray Sites α Abiogenesis & EvolutionAlgorithms of Evolution ¤ CancerCell Biology ~ Chemistry of Life Ω Complex Systems ººº CyanobacteriaEnzymesEvo Devo Ơ Fat ф Immunology »» Mechanisms of EvolutionMolecular Biology ** Origin of LifePaleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ SleepStromatolitesTaxonomy Phylogeny ۰۰ Virus • White Sites  Diagrams & Tables æ Eubacteria & Archaea φ MoleculeMolecular Paths ››› PathwaysPhotosynthesis • Black Sites Ǒ Endosymbiosis ō Organics

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photosynthesis tables

 Overview of Photosynthesis
 Structure of bacteriochlorophylls
 Comparison of Photosynthesis and Respiration
 Comparison of Plant and Bacterial Photosynthesis
 Comparison of C-3, C-4, CAM plants

• • Section PhotosynthesisCalvin cycleC-3C-4CAMChloroplastChlorosomesCyanobacterial cellMitochondriaPhycobilisomes : cyclic photophosphorylation : • Light-reactions : noncyclic photophosphorylation : • Nonoxygenic photosynthesisOxygenic photosynthesisPhotosynthesis OverviewPhotophosphorylationPhycobilisomesPlant cellTimeline •• • Section PigmentsAntenna and Reaction CenterBacteriochlorophyllsbacteriochlorophyllsbeta-carotene •• Carotenoidscarotenoidschlorophyll •• Chlorophylls and accessory pigmentsPigments and absorption spectraPhycobilinsphycocyaninphycoerythrinPhycobilisomes

Alphabetic links to Glossary items:
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Companion Sites : Gray Sites α Abiogenesis & EvolutionAlgorithms of Evolution ¤ CancerCell Biology ~ Chemistry of Life Ω Complex Systems ººº CyanobacteriaEnzymesEvo Devo Ơ Fat ф Immunology »» Mechanisms of EvolutionMolecular Biology ** Origin of LifePaleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ SleepStromatolitesTaxonomy Phylogeny ۰۰ Virus • White Sites  Diagrams & Tables æ Eubacteria & Archaea φ MoleculeMolecular Paths ››› PathwaysPhotosynthesis • Black Sites Ǒ Endosymbiosis ō Organics

| 0 Guide-Glossary

prokaryote tables

 Comparisons of Eubacteria, Archaea, and Eukaryotes
 Cell walls of Prokaryotes
 Electron acceptors for respiration and methanogenesis in prokaryotes
 Gene Regulation in E.coli
 Glycolysis in bacteria
 Lithotrophic prokaryotes
 Structure of bacteriochlorophylls
 Comparison of Plant and Bacterial Photosynthesis

æ StructureProkaryote structureCell wall
æ Taxonomy & PhylogenyTaxonomy and PhylogenyEubacteriaThe Archaea
æ Physiology & CommunicationInteractions in BacteriaBacterial motilitychemotactic signaling, chemotaxisPhosphorylation switchesPhotosynthetic bacteria
æ Genetics & BiochemistryControl of gene expressionRecombinant DNA Restriction Enzmes Restriction EndonucleasesStress genes, proteins, molecular chaperonesHorizontal Gene TransferConjugationTransductionTransformationSymbiosis
æ PhylaDomainsKingdomsPhylumDivisionAquifexThermotogaGreen nonsulfurDeinococcusBacteroides-FlavobacteriaPlanctomycesGram-positiveChlamydiaCyanobacteriaSpirochetesGreen sulfurProteobacteriagreen filamentousgreen phototrophicgreen sulfurgreen nonsulfurprochlorophytespurple sulfurpurple nonsulfurRickettsiales • (sulfur bacteria) • Nanoarchaeota ae

۰۰ DNA viruses ۰۰ retroviruses ۰۰ RNA viruses ۰۰ viral replication ۰۰

Alphabetic links to Glossary items:
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Companion Sites : Gray Sites α Abiogenesis & EvolutionAlgorithms of Evolution ¤ CancerCell Biology ~ Chemistry of Life Ω Complex Systems ººº CyanobacteriaEnzymesEvo Devo Ơ Fat ф Immunology »» Mechanisms of EvolutionMolecular Biology ** Origin of LifePaleogeology ¿ Refuting ID ǒ Serial Endosymbiosis ζζ SleepStromatolitesTaxonomy Phylogeny ۰۰ Virus • White Sites  Diagrams & Tables æ Eubacteria & Archaea φ MoleculeMolecular Paths ››› PathwaysPhotosynthesis • Black Sites Ǒ Endosymbiosis ō Organics

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. . . since 10/06/06