Table of Contents
Biology & Medical Biology
The living cell
Revolution: genomics and bioinformatics
Does all that DNA explain Life?
No!
Now important: Integrative Biology
What is BioComplexity?
Biology: integration at multiple levels
Molecular Cell Physiology: where Life begins
Molecular Cell Physiology: Structure of the course
Molecular Cell Physiology: Contents
Introduction
Ever noticed?
The Cell: dead structures
The Cell: live processes
The living cell needs processes in order to maintain its structures
The living cell needs structures in order to maintain its processes
1. From thermodynamics to metabolic pathways, and beyond Life as a flux driven system
The cell as a ‘flux-driven’ system
Gibbs energy dissipation drives processes
The cell as a flux driven system
Where are we?
1. Biology: from thermodynamics to metabolic pathways, and beyond
Energetics; no free lunch: Gibbs energy transduction needed
Energetics: Downhill in terms of driving force
Energetics: Downhill in terms of driving force
Energetics: Downhill in terms of driving force
Energetics; downhil and uphill
?GATPhydrolysis
Energetics; uphill ATP synthesis driven by proton gradient
Total force on proton
Energetics; towards proton gradient
Redox potential difference
Energetics; redox input
From electron (redox) to proton to ATP
1. Biology: from thermodynamics to metabolic pathways, and beyond
Metabolic network: Small molecules (?) interconverted by enzymes (-)
Main laws of biochemistry
In short: Life=f(processes(enzymes(genes)))
How do enzymes communicate? Structure or reactivity?
How do enzymes communicate? Reactivity
Enzym kinetics
Implication of enzyme steady state
Michaelis constant, KM
Reaction rate:
Michaelis/Menten equation: [P]=0
Kinetics; zero product
Elasticity coefficient: extent of listening
Listening is not always the same: 1 or 0
Substrate elasticity zero product
Listening is not always the same: 1 or 0
Kinetics; product not zero
Listening is not always the same: 1 or 0
Kinetics: relationship between kinetic constants
Rate as a function of driving force
How does a rate depend on its driving force?
Concluding about flow-force relations
1. Biology: from thermodynamics to metabolic pathways, and beyond
Enzyme systems at steady state
Enzyme systems at steady state
How important is each enzyme for steady state performance (flux, concentrations)?
1. Biology: from thermodynamics to metabolic pathways, and beyond
Metabolic Control Analysis: Introduction
Which enzyme determines the flux?
Criteria originally in use
Problems arising
Metabolic Control Analysis take 1
Metabolic Control Analysis
Metabolic Control Analysis
Control Coefficient
Flux Control Coefficient
Metabolic Control Analysis take 2
Three ways to determine a control coefficient
PPT Slide
Surprise: nobody and everyone was right: distributed control
Energetics; uphill ATP synthesis driven by proton gradient
But is it really that important?
Three ways to determine a control coefficient
Measurement of flux control: Tunable promoter
Tunable promoter up front H+-ATPase operon
Tunable promoter up front H+-ATPase operon
Example: Control by H+-ATPase: very small
Control by H+-ATPase: very small
Three ways to determine a control coefficient
Now we know how to measure the extent to which each enzyme controls the flux
How do enzymes communicate again?
Elasticity coefficient: extent of listening
Metabolic Control Analysis take 3
Metabolic Control Analysis: laws
The summation theorem for flux control
The connectivity theorem for flux control
Implication of summation plus connectivity theorem
The summation theorem for concentration control
The connectivity theorem for concentration control
Implications of summation plus connectivity theorem
Inversion law
Metabolic Control Analysis: laws
1. Biology: from thermodynamics to metabolic pathways, and beyond
PPT Slide
Control hierarchy: covalent modification/signal transduction
Hierarchical Control: Additional control!
Control hierarchy: gene expression
1. Biology: from thermodynamics to metabolic pathways, and beyond
Democratic Hierarchy
DNA supercoiling
From structure to function: calculating structure dynamics of DNA in the cell
DNA gyrase reduces Linking number in steps of two
Hierarchical Control Analysis
In vitro gyrase dependent supercoiling depends on [ATP]/[ADP]
In vivo gyrase dependent supercoiling depends on [ATP]/[ADP]
In vivo supercoiling depends on gyrase activity
In vivo supercoiling depends on topoisomerase I activity
Metabolic Control Analysis take 4
Hierarchical Control Analysis
Control distributed over levels
1. Biology: from thermodynamics to metabolic pathways, and beyond
Enzyme systems: kinetic modeling
Yeast glycolysis: How do the individual processes organize themselves and the cell?
Validated kinetic equation for each enzyme, e.g.:
Calculated fluxes and concentrations for yeast
Calculations versus experiment
Sustained glycolytic oscillations
Oscillations in yeast glycolysis: experimental
Active synchronization
Drunken cells singing in synchrony? Mechanisms
Drunken yeast cells towards dynamics: oscillating chemostat
Eukaryotic cell cycle oscillation
Oscillations:
Rational drug design; Trypanosomes
Glycosome glycolysis
Control of glycolysis
Everybody was looking at the wrong place:
1. Biology: from thermodynamics to metabolic pathways, and beyond
Molecular Cell Physiology: Contents
End of first week of lectures
|
Author: Hans V. Westerhoff
Email: hw@bio.vu.nl
Home Page: http://www.bio.vu.nl/hwconf
Other information:
Lectures first week of Molecular Cell Physiology, April 2001; Free University Amsterdam
|