1. Transcription direction RNA polymerase consensus sequence Initiation Elongation Termination α2ββ’σ σ = Initiation factor Promotor -35 = TTGACA -10 = TATAAT (Pribnow box) ρ dependent, independent Stem& Loop ρ Factor

3. Structural similarity between a bacterial RNA polymerase and a eucaryotic RNA polymerase II. Regions of the two RNA polymerases that have similar structures are indicated in green. The eucaryotic polymerase is larger than the bacterial enzyme (12 subunits instead of 5), and some of the additional regions are shown in gray. The blue spheres represent Zn atoms that serve as structural components of the polymerases, and the red sphere represents the Mg atom present at the active site, where polymerization takes place. The RNA polymerases in all modern-day cells (bacteria, archaea, and eucaryotes) are closely related, indicating that the basic features of the enzyme were in place before the divergence of the three major branches of life

5. Transcription Bubble. A schematic representation of a transcription bubble in the elongation of an RNA transcript. Duplex DNA is unwound at the forward end of RNA polymerase and rewound at its rear end. The RNA-DNA hybrid rotates during elongation.

6. The structure of a bacterial RNA polymerase
The structure of a bacterial RNA polymerase. Two depictions of the three-dimensional structure of a bacterial RNA polymerase, with the DNA and RNA modeled in. This RNA polymerase is formed from four different subunits, indicated by different colors (right). The DNA strand used as a template is red, and the non-template strand is yellow. The rudder wedges apart the DNA-RNA hybrid as the polymerase moves. For simplicity only the polypeptide backbone of the rudder is shown in the right-hand figure, and the DNA exiting from the polymerase has been omitted. Because the RNA polymerase is depicted in the elongation mode, the σ factor is absent

8. Schematic representation of the major form of E
Schematic representation of the major form of E. coli RNA polymerase bound to DNA. By convention, the transcription-initiation site is generally numbered +1. Base pairs extending in the direction of transcription are said to be downstream of the start site; those extending in the opposite direction are upstream. The σ70 subunit binds to specific sequences near the −10 and −35 positions in the promoter. The α subunits lie close to the DNA in the upstream direction. The β and β′ subunits associate with the start site

9. Alternative Promoter Sequences
Alternative Promoter Sequences. A comparison of the consensus sequences of standard promoters, heat-shock promoters, and nitrogen-starvation promoters of E. coli. These promoters are recognized by σ70, σ32, and σ54, respectively.

11. Members of the s70 family of sigma factors have 4 conserved regions
masks the DNA binding activities that are present in regions 2 and 4, which become unmasked when the sigma factor binds to the core RNA polymerase
Region 2
Subregion 2.3 and 2.4 form a DNA binding activity that recognizes the -10 promoter motif, region 2 also interacts with core enzyme components
Region 4:
a DNA binding activity that recognizes the -35 promoter motif

12. subunit size aa size (Kd) gene
function
alpha ()
329
36511
rpoA
required for assembly of the enzyme; interacts with some regulatory proteins; also involved in catalysis
beta (b)
1342
150616
rpoB
involved in catalysis: chain initiation and elongation
beta' (b')
1407
155159
rpoC
binds to the DNA template
sigma (s)
613
70263
rpoD
directs enzyme to the promoter
omega (w) 91
10237
rpoZ
required to restore denatured RNA polymerase in vitro to its fully functional form

14. principal sigma factor s54 rpoN (ntrA, glnF)
gene
function
s70
rpoD
principal sigma factor
s54
rpoN (ntrA, glnF)
nitrogen-regulated gene transcription
s32
rpoH
heat-shock gene transcription sS
 rpoS
gene expression in stationary phase cells sF
 rpoF
expression of flagellar operons sE
 rpoE
involved in heat shock and oxidative stress responses; regulates expression of extracytoplasmic proteins
sFecI
 fecI
regulates the fec genes for iron dicitrate transport

15. Sigma
Factor
Promoters Recognized
Promoter Consensus
−35 Region
−10 Region
σ70
Most genes
TTGACAT
TATAAT
σ32
Genes induced by heat shock
TCTCNCCCTTGAA
CCCCATNTA
σ28
Genes for motility and chemotaxis
CTAAA
CCGATAT
σ38
Genes for stationary phase and stress response ?
−24 Region
−12 Region
σ54
Genes for nitrogen metabolism and other functions
CTGGNA
TTGCA

16. Structure of the σ Subunit. The structure of a fragment from the E
Structure of the σ Subunit. The structure of a fragment from the E. coli subunit σ70 reveals the position of an α helix on the protein surface; this helix plays an important role in binding to the -10 TATAAT sequence.

21. RNA-DNA Hybrid Separation
RNA-DNA Hybrid Separation.      A structure within RNA polymerase forces the separation of the RNA-DNA hybrid, allowing the DNA strand to exit in one direction and the RNA product to exit in another

22. Mechanism For the Termination of Transcription by ρ Protein
Mechanism For the Termination of Transcription by ρ Protein. This protein is an ATP-dependent helicase that binds the nascent RNA chain and pulls it away from RNA polymerase and the DNA template.

23. Rho factor

24. Rho-dependent termination
Rho-dependent termination. Rho is a helicase that follows the RNA polymerase along the transcript. When the polymerase stalls at a hairpin, Rho catches up and breaks the RNA-DNA base pairs, releasing the transcript. Note that the diagram is schematic and does not reflect the relative sizes of Rho and the RNA polymerase.

25. Termination at an intrinsic terminator
Termination at an intrinsic terminator. The presence of an inverted palindrome in the DNA sequence results in formation of a hairpin loop in the transcript

26. Termination Signal. A termination signal found at the 3′ end of an mRNA transcript consists of a series of bases that form a stable stem-loop structure and a series of U residues

28. Rho Dependent Transcription Termination
Rho Independent Transcription Termination