BioMetabModeling

BioMetabModeling - Catabolism Precursors Inside every cell...

Info iconThis preview shows pages 1–19. Sign up to view the full content.

View Full Document Right Arrow Icon
Inside every cell atabolism rsors Nucleotides Catabolism Precu r Carriers Core metabolic bowtie
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Core metabolism atabolism rsors Nucleotides Catabolism Precu r Carriers Inside every ell ( 0 30 cell ( 10 )
Background image of page 2
atabolism rsors Catabolism Precu r Carriers
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Gly atabolism G1P G6P F6P Catabolism F1-6BP Gly3p 13BPG ATP TCA Pyr Oxa Cit ACA PEP 3PG 2PG NADH
Background image of page 4
Gly 1P G1P G6P ursors F6P 1 BP Prec u metabolites F1-6BP Gly3p 13BPG 3PG TCA Pyr Oxa ACA PEP 2PG Cit
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Gly 1P nzymatically G1P G6P Enzymatically catalyzed reactions F6P 1 BP F1-6BP Gly3p 13BPG 3PG TCA PEP Pyr 2PG Oxa ACA Cit
Background image of page 6
Gly 1P Autocatalytic G1P G6P F6P 1 BP consumed Rest of cell F1-6BP Gly3p ATP 13BPG 3PG produced TCA Pyr Oxa ACA PEP 2PG NADH Cit
Background image of page 7

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Gly 1P G1P G6P Feedbacks F6P 1 BP Autocatalysis F1-6BP Gly3p ATP Control 13BPG 3PG TCA PEP Pyr 2PG NADH Oxa ACA Cit
Background image of page 8
Gly G1P G6P F6P F1-6BP Gly3p 3BPG Oxa 13BPG 3PG TCA Pyr Cit ACA PEP 2PG
Background image of page 9

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Gly G1P Unreadable G6P F6P F1-6BP hy so complex? Gly3p 3BPG ATP Why so complex? 13BPG 3PG Oxa TCA PEP Pyr 2PG NADH Cit ACA
Background image of page 10
Hard tradeoffs • Speed vs efficiency vs robustness vs … • Existing theories limited to one dimension teful • Important tradeoffs are across these • Robustness most important for complexity was t • Thermodynamics (Carnot) slow • Communications (Shannon) • Control (Bode) omputation (Turing) ? • Computation (Turing) fragile
Background image of page 11

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Gly Feedbacks G1P 6P G6P F6P 1 BP Autocatalysis ontrol F1-6BP Gly3p 3BPG ATP Control 13BPG 3PG Oxa TCA PEP Pyr 2PG NADH Cit ACA
Background image of page 12
Gly G1P 6P G6P F6P 1 BP F6P 1 BP Autocatalysis ontrol F1-6BP Gly3p 3BPG ATP F1-6BP Gly3p Control 13BPG 3PG Oxa 3PG TCA PEP Pyr 2PG NADH Cit ACA
Background image of page 13

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
F6P consumed Rest of cell F1-6BP Gly3p 3BPG ATP lump 13BPG PG produced F6P 1 BP F6P 1 BP Control F1-6BP Gly3p 3BPG F1-6BP Gly3p Plus Autocatalytic 13BPG 3PG 3PG Feedback
Background image of page 14
F6P consumed Rest of cell F1-6BP Gly3p 3BPG ATP lump 13BPG PG produced autocatalytic nutrients 1 ah yy q    q, a h x y control 1 1 g kxy q   0 1 d g consumption waste
Background image of page 15

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
autocatalytic nutrients 1 ah yy q    q, a h 1 x d       x y control 0 1 g yq dt kxy        1 1 g kxy q   0 1 d g   1 1 d q consumption waste
Background image of page 16
0 0.2 Time Simulation 0 0.2 Time Simulation =5 6 -0.4 -0.2 6 -0.4 -0.2 h=3 h5 -1 -0.8 -0.6 -1 -0.8 -0.6 h=2,3,4 h=1 0 5 10 Time 0 5 10 1 ah yy q    q=a= 1 1 0 h y q=a= 0 k=3 x y h x y h 1 1 kx q  0 1 d  1 1 kx q 0 1 d
Background image of page 17

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
utrients Quantify tradeoffs ( x, y, d ) = signals autocatalytic nutrients ( q, a, k, h, g ) = “constants” omplexity 1 a h yy q    q, a h tl Complexity Enzymes Network x y control Metabolic Overhead Enzyme complexity 1 1 g kxy q  0 1 d  g Enzyme amount Autocatalysis aste/Nutrients consume aste
Background image of page 18
Image of page 19
This is the end of the preview. Sign up to access the rest of the document.

Page1 / 115

BioMetabModeling - Catabolism Precursors Inside every cell...

This preview shows document pages 1 - 19. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online