rna level/ transcription rate
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RNA level/ Transcription rate
form/activity
Enzyme level/Translation rate
Enzyme form/activity
Reaction rate
Proteins
RNAs
DNAs
level
form/activity
rate
level
form/activity
rate
rate
food intake
Organs
Tissues
Cells
Molecules
Robust
EvolvableEfficient
Inside every organism
Catabolism
Pre
curs
ors
Carriers
Co-factors
Fatty acids
Sugars
NucleotidesAmino Acids
Inside every cell
RNA level/ Transcription rate
DNA level
Biosynthesis
RNA
Gene
Transc.xRNA
RNAp
Pre
curs
ors
Co-factors
Fatty acidsSugars
Nucleotides
Amino Acids
Massively autocatalytic
Cat
abol
ism
AA
RNA
RNAp
Pre
curs
ors
Nucl.
AA
Gene
Transc.xRNA
Cat
abol
ism
AA
tRNA Ribosome
RNA
RNAp
transl. EnzymesPre
curs
ors
Nucl.
AA
Gene
Transc.xRNA
mRNAncRNA
Cat
abol
ism
AA
tRNA Ribosome
RNA
RNAp
Autocatalysis everywhere
transl. Enzymes
xRNAtransc.
Pre
curs
ors
Nucl.
AA
trans.EnzymesAA
mRNAncRNA
tRNA
Ribosome
RNA level/ Transcription rate
RNA form/activity
RNA
Gene
Transc.xRNA
RNAp
productsS reactions
Enz2
P
Enz1 reaction3
Enzyme level/Translation rate
Enzyme form/activity
Reaction rate
Enz2
trans.
ncRNATransc.
productsreactions
reaction3All products feedback
everywhere
These won’t be drawn in
detail
Proteins
trans.EnzymesAA
mRNAncRNA
tRNA
Ribosome
RNA level/ Transcription rate
RNA form/activity
RNA
Gene
Transc.xRNA
RNAp
productsS reactions
Enz2
P
Enz1 reaction3
Enzyme level/Translation rate
Enzyme form/activity
Reaction rate
Enz2
trans.EnzymesAA
mRNAncRNA
tRNA
Ribosome
RNA level/ Transcription rate
RNA form/activity
RNA
Gene
Transc.xRNA
RNAp
S reactionsP
Enz1 reaction3
Enzyme level/Translation rate
Enzyme form/activity
Reaction rate
Enz2
Mature red blood cells
live 120 days
Running only the top layers
productsS reactionsP
Enz1 reaction3 Enzyme form/activity
Reaction rate
Enz2
Genome
Application Diverse
Diverse
Diverse application
s and genomes
Archaea
Eukaryotes
Animals Fungi Plants
Bacteria Algae
What is locus of early evolution?
HGT andShared Protocols
Horizontal gene transfer
Archaea
Eukaryotes
Animals Fungi Plants
Bacteria Algae
DNA levelGene
Controlled, dynamic
HGT andShared Protocols
Horizontal gene transfer
Archaea
Eukaryotes
Animals Fungi Plants
Bacteria Algae
HGT andShared Protocols
trans.EnzymesAA
mRNA
ncRNAtRNARibosome
RNA level/ Transcription rate
RNA form/activity
RNA
Gene
Transc.xRNA
RNAp
productsS reactionsP
Enz1 reaction3
Enzyme level/Translation rate
Enzyme form/activity
Reaction rate
Enz2
Catabolism
Pre
curs
ors
Carriers
Co-factors
Fatty acids
Sugars
NucleotidesAmino Acids
Core metabolism
Co-factors
Fatty acids
Sugars
NucleotidesAmino Acids
Catabolism
Pre
curs
ors
Taxis and transport
Nut
rien
ts
Carriers
Core metabolism
Huge Variety
Same 12
in all cells
Same 8
in all cells
100
same
in all
organism
s
Catabolism
Pre
curs
ors
Carriers
Co-factors
Fatty acids
Sugars
NucleotidesAmino Acids
Core metabolism
Protocols
Constraints that deconstrain
Catabolism
Pre
curs
ors
Carriers
Co-factors
Fatty acids
Sugars
NucleotidesAmino Acids
Core metabolism
Catabolism
Pre
curs
ors
Carriers
Catabolism
TCAPyr
Oxa
Cit
ACA
Gly
G1P
G6P
F6P
F1-6BP
PEP
Gly3p
13BPG
3PG
2PG
ATP
NADH
TCAPyr
Oxa
Cit
ACA
Gly
G1P
G6P
F6P
F1-6BP
PEP
Gly3p
13BPG
3PG
2PG
Pre
curs
ors
metabolites
Enzymatically catalyzed reactions
TCA
Gly
G1P
G6P
F6P
F1-6BP
PEP Pyr
Gly3p
13BPG
3PG
2PG
Oxa
Cit
ACA
TCAPyr
Oxa
Cit
ACA
Gly
G1P
G6P
F6P
F1-6BP
PEP
Gly3p
13BPG
3PG
2PG
ATP
Autocatalytic
NADH
Pre
curs
ors
Carriers
TCA
Gly
G1P
G6P
F6P
F1-6BP
PEP Pyr
Gly3p
13BPG
3PG
2PG
ATP
NADH
Oxa
Cit
ACA
Regulatory
TCAPyr
Oxa
Cit
ACA
Gly
G1P
G6P
F6P
F1-6BP
PEP
Gly3p
13BPG
3PG
2PG
TCA
Gly
G1P
G6P
F6P
F1-6BP
PEP Pyr
Gly3p
13BPG
3PG
2PG
ATP
NADH
Oxa
Cit
ACA
If we drew the feedback loops the diagram would be unreadable.
( )
Mass &Reaction
Energyflux
Balance
dxSv x
dt
Stoichiometry or mass and energy balance
Nutrients Products
Internal
Biology is not a graph.
( )
Mass &Reaction
Mass&Energy Energyflux
Balance
dxSv x
dt
d
dt
Stoichiometry plus regulation
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 (?!?)
TCA
Gly
G1P
G6P
F6P
F1-6BP
PEP Pyr
Gly3p
13BPG
3PG
2PG
ATP
NADH
Oxa
Cit
ACA
( )
Mass &Reaction
Energyflux
Balance
dxSv x
dt
Stoichiometry matrix
S
Regulation of enzyme levels by transcription/translation/degradation
TCA
Gly
G1P
G6P
F6P
F1-6BP
PEP Pyr
Gly3p
13BPG
3PG
2PG
Oxa
Cit
ACA
( )
Mass &Reaction
Energyflux
Balance
dxSv x
dt
level
TCA
Gly
G1P
G6P
F6P
F1-6BP
PEP Pyr
Gly3p
13BPG
3PG
2PG
ATP
NADH
Oxa
Cit
ACA
( )
Mass &Reaction
Energyflux
Balance
dxSv x
dt
Allosteric regulation of enzymes
form/activity
TCA
Gly
G1P
G6P
F6P
F1-6BP
PEP Pyr
Gly3p
13BPG
3PG
2PG
ATP
NADH
Oxa
Cit
ACA
Mass &Reaction
( ) Energyflux
Balance
dxSv x
dt
level
form/activity
rate
TCA
Gly
G1P
G6P
F6P
F1-6BP
PEP Pyr
Gly3p
13BPG
3PG
2PG
ATP
NADH
Oxa
Cit
ACA
Fast response
Slow
level
form/activity
rate
Layered architecture
Mass &Reaction
( ) Energyrate
Balance
dxSv x
dt
Enzyme level/Translation rate
Enzyme form/activity
Reaction rate
Proteins
RNAs
DNAs
level
form/activity
rate
Control of
protein levels
RNA level/ Transcription rate
form/activity
Enzyme level/Translation rate
Enzyme form/activity
Reaction rate
Proteins
RNAs
DNAs
level
form/activity
rate
level
form/activity
rate
rate
RNA level/ Transcription rate
DNA level
RNA
Gene
Transc.xRNA
RNAp
Transcription
RNA level/ Transcription rate
DNA level
RNA level
RNA
Gene
Transc.xRNA
RNAp
product
Enz
Controlled, dynamic
RNA level/ Transcription rate
DNA level
RNA
Gene
Transc.xRNA
RNAp
trans.EnzymesAA
mRNA ncRNAtRNA
Pre
curs
ors
Nucl.
AA Enzyme level/Translation rate
trans.EnzymesAA
mRNA
ncRNAtRNARibosome
RNA level/ Transcription rate
RNA form/activity
RNA
Gene
Transc.xRNA
RNAp
productsS reactionsP
Enz1 reaction3
Enzyme level/Translation rate
Enzyme form/activity
Reaction rate
Enz2
RNA level/ Transcription rate
RNA form/activity
Enzyme level/Translation rate
Enzyme form/activity
Reaction rateWhat to call
the sublayers?
level
form/activity
rate
What is where
Genes
Co-factorsFatty acidsSugars
Nucleotides
Amino Acids
Polymerization and complex
assemblyP
roteinsP
recu
rsor
s
Autocatalytic feedback
Taxis and transport
Nut
rien
ts
Core metabolism
DNA replication
Trans*
Cat
abol
ism
Carriers
100 104 to ∞in one
organisms
Huge Variety
12
8
Polymerization and complex
assembly
Autocatalytic feedback
Genes
ProteinsDNA
replication
Trans*
104 to ∞in one
organismsHuge
VarietyFew polym
erases
Highly conserved
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