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Mathematical Modeling of Networks
Regulatory Networks (continued)
Dynamics of Reactions
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Michaelis Menten Kinetics
Dynamics of Reactions
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Michaelis Menten Kinetics
Dynamics of Reactions
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Michaelis Menten Kinetics
Dynamics of Reactions
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Michaelis Menten Kinetics
Dynamics of Reactions
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Michaelis Menten Kinetics
Dynamics of Reactions
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Beyond Michaelis Menten Kinetics
Dynamics of Reactions
Dynamics of Reactions
Dynamics of Reactions
What we can build with this
machinery?
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Genetic switches
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Chemotaxis
Genetic Switches
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Life-cycle of a bacteriophage
A bacteriophage (from 'bacteria' and Greek
φάγειν phagein "to eat") is any one of a number
of viruses that infect bacteria.
Bacteriophages may have a lytic cycle or a
lysogenic cycle, but a few viruses are capable
of carrying out both.
With lytic phages such as the T4 phage,
bacterial cells are broken open (lysed) and
destroyed after immediate replication of the
virion. As soon as the cell is destroyed, the new
Genetic Switches
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In Lysogenic cycle, the viral genome integrates
with host DNA and replicates along with it fairly
harmlessly.
The virus remains dormant until host conditions
deteriorate, perhaps due to depletion of
nutrients, then the endogenous phages (known
as prophages) become active.
At this point they initiate the reproductive cycle
resulting in lysis of the host cell.
As the lysogenic cycle allows the host cell to
continue to survive and reproduce, the virus is
Genetic Switches
Genetic Switches
Genetic Switches
Genetic Switches
Genetic Switches
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The lambda repressor gene system consists of
(from left to right on the chromosome):
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cI gene
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OR3
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OR2
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OR1
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cro gene
Genetic Switches
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The life cycle of lambda phages is
controlled by cI and Cro proteins. The
lambda phage will remain in the
lysogenic state if cI proteins
predominate, but will be transformed
into the lytic cycle if cro proteins
predominate.
The cI dimer may bind to any of three
Protein Structure Overview
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cro; (Control of Repressor's Operator)
Transcription inhibitor, binds OR3,
OR2 and OR1 (affinity OR3 > OR2 =
OR1)
cI; (Clear 1) Transcription inhibitor,
binds OR1, OR2 and OR3 (affinity
OR1 > OR2 = OR3, ie. preferentially
binds OR1). Susceptible to cleavage
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How do we build mathematical models?