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rate form/activity level rate form/activity level rate Reaction rate Enzyme form/activity Proteins Enzyme level/ Translation rate form/activity RNAs RNA level/ Transcription rate DNAs Inside every organism food intake Robust Efficient Evolvable Organs Tissues Cells Molecules Catabolism Precursors Inside every cell Carriers Nucleotides Precursors Biosynthesis Massively autocatalytic Co-factors RNA Transc. xRNA RNA level/ Transcription rate RNAp Gene DNA level Precursors Catabolism AA RNA Transc. Gene xRNA RNAp Precursors Catabolism AA transl. tRNA Enzymes Ribosome ncRNA mRNA RNA Transc. Gene xRNA RNAp Precursors Catabolism AA transl. Enzymes tRNA Autocatalysis everywhere Ribosome RNA transc. xRNA RNAp S reactions P Enz1 reaction3 tRNA ncRNA AA trans. products Reaction rate Enzyme form/activity Enz2 Enzyme level/ Translation rate Enzymes Enz2 RNA form/activity mRNA RNA Transc. Gene RNAp xRNA RNA level/ Transcription rate Ribosome reactions All products feedback everywhere products reaction3 Proteins trans. These won’t be drawn in detail Transc. ncRNA S reactions P Enz1 reaction3 tRNA ncRNA AA trans. products Reaction rate Enzyme form/activity Enz2 Enzyme level/ Translation rate Enzymes Enz2 RNA form/activity mRNA RNA Transc. Gene RNAp xRNA RNA level/ Transcription rate Ribosome S reactions P Enz1 reaction3 tRNA ncRNA AA trans. Reaction rate Enz2 Enzymes Enzyme form/activity Enzyme level/ Translation rate RNA form/activity mRNA RNA Transc. Gene RNAp xRNA RNA level/ Transcription rate Ribosome S reactions Enz1 reaction3 P products Reaction rate Enz2 Enzyme form/activity Running only the top layers Mature red blood cells live 120 days Diverse Application Diverse application s and genomes Genome Diverse Horizontal gene transfer HGT and Shared Protocols Bacteria Eukaryotes Animals Archaea Fungi Plants Algae What is locus of early evolution? Horizontal gene transfer HGT and Shared Protocols Bacteria Eukaryotes Animals Archaea Gene Fungi Plants Algae DNA level Controlled, dynamic reactions S HGT and Shared Protocols Bacteria products Reaction P rate Eukaryotes Enz1 reaction3 Enz2 Animals Fungi Plants Archaea AA trans. Enzyme form/activity Enzyme level/ Enzymes Translation rate Algae mRNA Ribosome tRNA RNA Transc. RNAp ncRNA xRNA Gene RNA form/activity RNA level/ Transcription rate Catabolism Precursors Core metabolism Carriers Nucleotides Catabolism Precursors Nutrients Taxis and transport Same 12 in all Core metabolism cells Nucleotides Carriers Same 8 in all cells Catabolism Precursors Core metabolism Nucleotides Carriers Constraints that deconstrain Protocols Catabolism Precursors Core metabolism Carriers Nucleotides Precursors Catabolism Carriers Gly G1P G6P Catabolism F6P F1-6BP Gly3p ATP 13BPG 3PG 2PG NADH Oxa PEP Pyr ACA TCA Cit Gly Precursors G1P G6P F6P metabolites F1-6BP Gly3p 13BPG 3PG 2PG Oxa PEP Pyr ACA TCA Cit Gly G1P G6P Enzymatically catalyzed reactions F6P F1-6BP Gly3p 13BPG 3PG 2PG Oxa PEP Pyr ACA TCA Cit Gly Precursors G1P G6P F6P Autocatalytic F1-6BP Gly3p Carriers ATP 13BPG 3PG 2PG Oxa PEP Pyr ACA TCA NADH Cit Gly G1P G6P Regulatory F6P F1-6BP Gly3p ATP 13BPG 3PG 2PG Oxa PEP Pyr ACA TCA NADH Cit Gly G1P G6P F6P F1-6BP Gly3p 13BPG 3PG 2PG Oxa PEP Pyr ACA TCA Cit If we drew the feedback loops the diagram would be unreadable. Gly G1P G6P F6P F1-6BP Gly3p ATP 13BPG 3PG 2PG Oxa PEP Pyr ACA TCA NADH Cit Stoichiometry or mass and energy balance Biology is not a graph. dx Sv( x) dt Mass & Reaction Energy flux Balance Interna l Nutrients Products dx Sv( x) dt Stoichiometry plus regulation Mass & Reaction d Mass&Energy Energy flux dt Balance Matrix of integers “Simple,” can be known exactly Amenable to high throughput assays and manipulation Bowtie architecture Vector of (complex?) functions Difficult to determine and manipulate Effected by stochastics and spatial/mechanical structure Hourglass architecture Can be modeled by optimal controller (?!?) dx S Sv( x) dt Mass & Reaction Energy flux Balance Gly G1P G6P F6P F1-6BP Gly3p ATP Stoichiometry matrix 13BPG 3PG 2PG Oxa PEP Pyr ACA TCA NADH Cit dx Sv( x) dt Mass & Reaction Energy flux Balance Gly G1P G6P F6P F1-6BP Gly3p Regulation of enzyme levels by transcription/translation/degradation 13BPG 3PG 2PG Oxa PEP level Pyr ACA TCA Cit dx Sv( x) dt Mass & Reaction Energy flux Balance Gly G1P G6P F6P F1-6BP form/activity Gly3p ATP 13BPG Allosteric regulation of enzymes 3PG 2PG Oxa PEP Pyr ACA TCA NADH Cit Mass & Reaction dx Sv( x) Energy flux dt Balance Gly G1P G6P rate F6P form/activity F1-6BP Gly3p level ATP 13BPG 3PG 2PG Oxa PEP Pyr ACA TCA NADH Cit Mass & Reaction dx Sv( x) Energy rate dt Balance Gly G1P G6P rate F6P Layered F1-6BP architecture Gly3p form/activity level ATP 13BPG 3PG 2PG Oxa PEP Pyr ACA TCA NADH Cit rate form/activity level Control of protein levels Reaction rate Enzyme form/activity Proteins Enzyme level/ Translation rate RNAs DNAs rate form/activity level rate form/activity level rate Reaction rate Enzyme form/activity Proteins Enzyme level/ Translation rate form/activity RNAs RNA level/ Transcription rate DNAs Transcription RNA Transc. RNAp Gene xRNA RNA level/ Transcription rate DNA level RNA level product Enz Controlled, dynamic RNA Transc. RNAp Gene xRNA RNA level/ Transcription rate DNA level Precursors AA tRNA trans. mRNA RNA Transc. RNAp Enzyme level/ Enzymes Translation rate Gene xRNA ncRNA RNA level/ Transcription rate DNA level reactions S Enz1 reaction3 AA trans. products Reaction P rate Enzyme form/activity Enz2 Enzyme level/ Enzymes Translation rate mRNA Ribosome tRNA RNA Transc. RNAp ncRNA xRNA Gene RNA form/activity RNA level/ Transcription rate What to call the sublayers? Reaction rate Enzyme form/activity rate form/activity level What is where Enzyme level/ Translation rate RNA form/activity RNA level/ Transcription rate Taxis and transport Autocatalytic feedback 12 Polymerization and complex assembly Precursors Catabolism Co-factors Genes Carriers DNA replication Huge Variety 8 100 Trans* Proteins Nutrients Core metabolism 104 to ∞ in one organisms Autocatalytic feedback Polymerization and complex assembly Huge Variety Proteins Genes DNA replication Trans* 104 to ∞ in one organisms
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