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Lecture 1
The lac operon: essential features of a genetic
regulatory circuit for an inductive system
Thursday, 1 November 2012
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DNA
RNA
Proteins
Thursday, 1 November 2012
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1
2
5
3
4
C
John Gurdon cloning experiments with XenopusGenetic information is not lost during development and can be recalled upon demand.
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DNA
RNA
Proteins
?
?
Thursday, 1 November 2012
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Genetics
Biochemistryand Cell Biology
Thursday, 1 November 2012
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•The Lac operon decides to use or not to use lactose
•The λ phage deciding whether to sail or to jump in an E. coli cell
•Galactose utilization in yeast
•Making stripes in the Drosophila embryo
Thursday, 1 November 2012
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•The Lac operon decides to use or not to use lactose
•The λ phage deciding whether to sail or to jump in an E. coli cell
•Galactose utilization in yeast
•Making stripes in the Drosophila embryo
Thursday, 1 November 2012
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Glucose Lactose
Growth
[X]
X=
When presented with a mixture of glucose and lactose, E. coli uses glucose first.
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Glucose Lactose
+
+ +
+
-
- -
-
Not made
not made
Not made
Made
Growth substrate
ß-galactosidase
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Glucose Lactose Mutants
+
+ +
+
-
- -
-
Not made
Not made
Made
Made
Not made
Made
Made
Growth substrate
ß-galactosidase
not made
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ß-galactosidase permease transacetylaseRepressor
Z Y AI
The lac operon
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Repressor
Z Y AI P O
IPTG is an inducer which is not metabolized
Repressor
Allolactose
Lactose
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Glucoseonly
Lactoseonly
ß-galactosidase in
I
I
-
s
OFF ON
ONON
OFF OFF
Mutants
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Z Y AI P Oi -
Repressor mutants
This is a trans recessive mutant: if I is provided from another piece of DNA, it would work
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Z Y AI P Oi -
Repressor mutants
This is a trans recessive mutant: if I is provided from another piece of DNA, it would work
IPTGIPTG
i s
This is a trans dominant mutant: if I is provided from another piece of DNA, it would work
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Repressor
Z Y AI O
P O
!
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Glucoseonly
Lactoseonly
ß-galactosidase in
O c
s
OFF ON
ONON
OFF OFFO
WT
Mutants
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Repressor
Z Y AI P O
Operator mutants
Oc
The repressor cannot bind the operator. This is a cis dominant mutant: it only works on the DNA linked to the mutation.
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Repressor
Z Y AI P O
Operator mutants
Oc
The repressor cannot bind the operator. This is a cis dominant mutant: it only works on the DNA linked to the mutation.
O s
The repressor cannot unbind, even in the presence of IPTG. This is a cis dominant mutant: it only works on the DNA linked to the mutation.
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How to achieve Specificity and Uniqueness
Genome: 4.6 x 10 6
Average protein:DNA contact, 5/6bp
4 6= 5x103
4 11≈ 5x106 ⇒ 11bp binding site
Dimers (2x1) or combinations (1+1)
Repressor
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Z Y AI O
P O
!
Thursday, 1 November 2012
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NB: i- [Z(glucose)< Z (lactose)]
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Glucoseonly
Lactoseonly
ß-galactosidase in
CAP
OFF ON
“on”OFF
WT
Mutants
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Glucoseonly
Lactoseonly
ß-galactosidase in
CAP
OFF ON
“on”OFF
WT
Mutants
CAP: Catabolyte activator protein binds cAMP
Glucose cAMP
Glucose cAMP
CAP
CAP active
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σα
CAP + cAMP
Catabolite Activating Protein (CAP) when bound by cAMP forms a dimer and helps RNA polymerase
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σα
CAP + cAMP
Catabolite Activating Protein (CAP) when bound by cAMP forms a dimer and helps RNA polymerase
Mutations in the CAP coding gene result in low expression of ß-galactosidase in the absence of glucose and the presence of lactose
σα
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Glucose Lactose
Growth
[X]
X=
CAPOperator
Lac Promoter
Low High
Occupied Free
Off On
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CAP P O
Z Y A
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Glucose Lactose
Promoterin
glucose
+
+ +
+
-
- -
-
Lowly
Poised
Loaded
Growth substrate
ß-galactosidase
Not made
“not made”
Not made
Made
CAP
Low
Low to High
High
High
Lowly
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How do repressors and activators actually work?
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There is about four (4) molecules of the Repressor
per cell
Remember Avogadro’s number: one mole contains 6X10 molecules23
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Z Y Alactose
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Z Y Alactose
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Confinement within a cell
Polymerization
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Cooperativity: when the energetic outcome of two otherwise independent event is thermodynamically more stable than would be predicted from the individual and independent
events
Keq1, 2 is > Keq1 + Keq2
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LacI uses cooperativity to increase functionality
Classic Jacob Monod
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σα
CAP + cAMP
Catabolite Activating Protein (CAP) when bound by cAMP forms a dimer RECRUITS RNA polymerase and USING the weak interacting forces
enhances its functionality
Regulated recruitment; a variation on cooperativity
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Confinement within a cell
Polymerization
Cooperative interactions
Regulated recruitment(d)
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How to achieve Specificity and Uniqueness
Genome: 4.6 x 10 6
Average protein:DNA contact, 5/6bp
4 6= 5x103
4 11≈ 5x106 ⇒ 11bp binding site
Dimers (2x1) or combinations (1+1)
RepressorCAP
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Do bacteria have memories?
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ß-galactosidase
Lactose
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ß-galactosidase
Lactose
Please notice that there is a difference between measuring the ‘average’ amount of ß-gal and the number (fraction) of cells that for a given lactose concentration express ß-gal !!!!!!!!!!!
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memory in bacteria?
Lactose
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Z Y Alactose
There is about 1 molecule of the repressor
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Z Y Alactose
•There is about 1 tetramer of the repressor•The transacetylase (Y) determines the degree of function of I
Z Y A
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Z Y Alactose
low lactose low lactose
or
cell1
low lactose low lactose
cell2
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low lactose low lactose
or
cell1
low lactose low lactose
cell2
Z Y A Z Y A Z Y A
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Z Y A Z Y A Z Y A
low lactose low lactose
or
cell1
low lactose low lactose
cell2
I lacZYA
lactose Y
I lacZYA
lactose Y
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Z Y A Z Y A Z Y A
low lactose low lactose
or
cell1
low lactose low lactose
cell2
I lacZYA
lactose Y
I lacZYA
lactose Y
lac Operon
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That which is found to be true for E coli will be true for the elephant
J. Monod
Thursday, 1 November 2012
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Summary•Genetics is a tool that allows us to access mechanisms
•Phenotypic decision making is underpinned by genetic networks
•Genetic networks have a biochemical basis
•Molecular principles of biological processes1. Regulation of local concentration through confinement or polymerization2. Cooperativity3. Regulated recruitment4. Network organization and activity
•In the end all is an evolutionarily selected combination of “Chance and Necessity”
Thursday, 1 November 2012