Académique Documents
Professionnel Documents
Culture Documents
1
Prokaryotic Cells
3 um
http://www.ucmp.berkeley.edu/bacteria/bacteriamm.html 2
Prokaryotic Cells
http://atlas.arabslab.com
3
Comparison to Eukaryotic Cells
http://www.cod.edu/people/faculty/fancher/ProkEuk.htm 4
Biochemistry
• Nucleic Acids (DNA, RNA)
• Proteins Replication
DNA
• Lipids
Transcription
• Carbohydrates RNA
• Small Molecules Translation
• Ions Protein
Metabolism Structural
Control
5
Biochemistry
Average spacing between proteins:
7 nm/molecule
Diameter of a protein: 5 nm
Replication
DNA
Transcription
RNA
Translation
Protein
Metabolism Structural
Control
David S. Goodsell (Scripps) 6
DNA
Replication
DNA
Transcription
RNA
Translation
Protein
Metabolism Structural
Control
7
DNA
Replication
DNA
Transcription
RNA
Translation
Protein
Metabolism Structural
Control
8
DNA
9
RNA
10
RNA
11
RNA Polymerase
mRNA
5’ end
http://mgl.scripps.edu/people/goodsell/pdb/pdb40/pdb40_1.html
12
Single Gene
Smallest Genome – was in 1999
}
This genome is of interest to synthetic biology because Craig Venter wants to use
this organism as the basis for a minimal organism for genetic engineering.
Venter’s group has removed roughly 101 genes and the organism is still viable,
the idea then is to patent the minimal set of genes required for life.
15
But the real prize goes to….
The 160-Kilobase Genome of the
Bacterial Endosymbiont Carsonella
Alanine: 350,000
Pyruvate: 370,000
ATP: 2,000,000
Ca ions: 2,300,000
Fe ions: 7,000,000
Glycolysis
Phosphofructokinase: 1,550
Pyruvate Kinase: 11,000
Enolase: 55,800
Phosphoglycerate kinase: 124,000
Krebs Cycle
Malate Dehydrogenase: 3,390
Citrate Synthase: 1,360
Source: Protein abundance profiling of the Escherichia coli cytosol.
BMC Genomics 2008, 9:102. Ishihama et al.
Aconitase: 1630 18
Circular Chromosome in E. coli
Page 231
19
EcoCyc: http://ecocyc.org/
20
E. coli Gene Structure
Stop codon
(TAG, TAA, TGA)
Start codon
Page 134 21
RNA Polymerase Binds to Promoters
mRNA
Changes in the promoter sequence
can change the efficiency of RNA
polymerase binding to the DNA.
http://mgl.scripps.edu/people/goodsell/pdb/pdb40/pdb40_1.html
22
Strong and Weak Promoters
The strength of a promote is one of the factors which
determines the rate of transcription.
TTGATA -- 16 -- TATAAT
TTGACA -- 17 -- TATAAT Most common Promoter
(Consensus sequence)
It differs from the averaged promoter sequence by one nucleotide and on base
pair in the spacer region.
23
Changes in the terminator sequence
RNA Polymerase Stops at a can change the efficiency of RNA
polymerase stopping. If the gene is
Terminator part of an operon, terminators can
modulate relative expression levels of
the different genes in the operon.
24
Operon Structure
25
Operators – Regulating Expression
26
Gene Regulation
lac Operon
Promoter
Promoter
Operator
Sugar in Medium Relative β-
galactosidase
lacZ codes for β-galactosidase.
lacY codes for β-galactoside permease. Glucose 1
Glucose + lactose 50
Lactose 2500
27
Gene Regulation
lac Operon
Lac repressor
Promoter Promoter
Operator
28
Gene Regulation
lac Operon
Lactose is galactose-(β1->4)-glucose, whereas
allolactose is galactose-(β1->6)-glucose.
31
Lac Operon Wiring Diagram
Allolactose
Lactose Internal
Lactose External
32
Lac Operon Wiring Diagram
Operator Lac Genes
Lactose
Internal
Lactose
External
33
Lac Operon Wiring Diagram
Operator Lac Genes
1
LI E
LE
34
Lac Operon Wiring Diagram
Operator Lac Genes
2
LI E
LE
35
Lac Operon Wiring Diagram
Operator Lac Genes
LI E
3
LE
36
Lac Operon Wiring Diagram
Operator Lac Genes
LI E
LE
37
Lac Operon Wiring Diagram
Operator Lac Genes
LI E
Two state variables: LI and E
Seven Parameters: k1, k2, k3, k4, Eo, n, Km
LE
What about LE ?
2 1
LI E
3
LE
39
Lac Operon Wiring Diagram
Operator Lac Genes
LI E p = defn cell
E -> $W; k1*E; // Enzyme degradation
LI -> $W; k2*E*LI; // Lactose metabolism
LE -> LI; k3*E*LE; // Lactose transport
$G -> E; Eo + k4*LI^n/(Km1 + LI^n); // Lac expression
end;
LE p.n = 2;
p.LE = 5;
p.Eo = 0.01;
p.Km1 = 0.5;
p.k1 = 0.1; p.k2 = 0.1;
p.k3 = 0.1; p.k4 = 0.1;
p.E = 0; p.LI = 0;
LI E
LE
41
Lac Operon Wiring Diagram
Operator Lac Genes
LI E
LE
42
Where did the gene expression rate
law come from?
Fit this data to the above equation, this yields a workable equation
43
Ribosome Binding Sites
44
In summary
5’- UTR
http://www.biotapestry.org/ 46
Protein Signaling Maps
47
Protein Signaling Maps
20% of the human protein-coding
genes encode components of signaling
pathways, including transmembrane
proteins, guanine-nucleotide binding
proteins (G proteins), kinases,
phosphatases and proteases.
48
Metabolic Maps
49