In the general comparison of prokaryotic and eukaryotic transcription a look into the mechanism and structures of both complexes was analyzed. Here a detailed look into the transcription process of eukaryotic polymerase II (pol II or RNAP II) is the focus. The process of transcription can be broken into three parts coinciding with different conformations and protein association with the core and holo-enzyme polymerase pol II (holo-RNAP), initiation, elongation and termination. Keeping in mind that the goal of this process in pol II is synthesis of an RNA transcript from a DNA template. Lets look at the details of each of these three steps starting at the beginning with initiation moving to elongation and ending in termination of the transcript RNA.

Commissioned by transcription activators assembly of the process begins. Necessary recruitment of the transcription factors (TF); IIA, IIB, IID(TBP), IIE, IIF, and IIH and RNAPII elements, (Rpb1-12) to form the initiation complex are needed. DNA contains promoter sequences that regulate the binding of the holo-RNAPII complex to the upstream sequence of the intended gene of transcript. The TATA box is one such sequence. It contains a -35, (5-TATATAAG-3) sequence optimal for the recognition of the first protein/DNA interactions by the TBP and TFIIB, tata binding proteins. (Kim et al. 1997)

TBP is the first to interact with the DNA it forms a structure similar to a saddle. The n-terminal domain of TBP contacts the 3( end of TATA and the C-terminal domain the 5( end of TATA. The saddle formation is formed by ten anti-parallel ( sheets eight of which contact the minor groove on the DNA. These interactions rely on hydrophobic interactions to stabilize the holo-RNAPII entering double helix DNA strand. The binding interactions of TBP bend the DNA and allow TFIIB to bind and both interact. Binding of the second initiation element TFIIB to TBP gives rise to the previously mentioned DNA bending hydrogen bonding interactions of TBP. They cause the DNA to bend around the C-terminal end (residues 120-345) of IIB (IIBc). TFIIB interacts with (-39 and -12) and TBP (-33 and -22) upstream promoter DNA nucleotides. The Asn69 and 159 residues interact with O2 and N3 of T5( and A5( and Thr125 and 215 residues interact with the N3's of A5( and A4, Phe190 and 207 interact with O4, (T1) and N6, (A2) DNA nucleotide base pairs. The N-terminal end of IIB, (IIBn) interacts with the RNAP RPb1 subunit docking motif through a motif called the Zinc ribbon in residues 409-419. The IIBn also has a finger domain (55-88) that extends passed the clamp and wall motif and into the active site of pol II. This finger comes in close contact with nucleotides -6 through - at the contained residues 62- 66 the "side of finger", 69 -74 the "fingertip". 62- 66 are intamitely involved in start site selection. Residue Arg78 forms a salt bridge with Glu62. These residues are on opposite sides of the finger motif, and the hydrogen bonding interactions of these two residues maintains the conformation of the finger due to the lack of secondary structure. (6) Between the IIBn finger motif and IIBc regions there is a linker domain (88-120) which interacts with the zinc ribbon, allowing it to bind the emerging complex. A, like omega in Bpol is an initiation complex stabilizer and binds to this forming complex.

The remaining subunits, E, F, and H are now able to interact with the bound TBP-TFIIB-RNAP complex. E, F and H have detailed roles yet to come. TFIIF is essential for RNAP to bind and it forms a tight complex with the Rpb4/7 region of RNAPII. This Rpb4/7 region of RNAP is closely associated with the large subunit of TFIIF. These interactions help bridge the core polymerase and the transcription initiation factors contributing to promoter specificity. (9) A second feature of Rpb4/7 is that it is responsible for the locking of the clamp formation open by interacting with five movable domains or "switches that allow the clamp to rotate and close. It associates with a pocket formed by Rpb 1and 2.

The movement of this clamp region into the closed position is related to the beta unit of Bpol that conatins the lid and rudder motifs. RNAP clamp indeed has three loops that extend out from it, termed the lid, rudder and zipper. These loops are believed to interact with the transcription bubble and are controlled by five switches. Transcription factors H and E interact with the core to initiate these switches. Rpb1 contains switch 1, 2 and 5 while Rpb2 has switches 2, 3 and 4. Switch 1 is in the cleft-clamp core domain, resides 1384-1406, and when activated two short helices are formed. (47a and 47b) Switch 2 is in the clamp core, residues 328-346 and when activated the helical turn flips out. Switch three a 1107-1129 loop hybrid binding anchor, becomes order. Switch 4, in the clamp domain anchor region, 1152-1159 gets one turn added to helix 32. The last switch to activate and close the clamp domain is switch five, which is in the clamp core 1431-1433, acts like a hinge and is able to bend. Closing of the clamp structure and the separation of the template and non-template DNA, forming the transcription bubble forces the template DNA under the clamp and over the helix bridge. Template nucleotides +4 +3 and +2 are stacked in right handed DNA, +1 is flipped with respect to +2, by a left handed twist of 90 degrees. This base when flipped points downward into the bottom of the cleft making readout possible for the active site. This is possible from the binding interactions of switches 1 and 2 as well as the bridge helix. The fork-loop strands in Rbp2 1 and 2 help stabilize the end and a little upstream of the transcription bubble.
Addition of nucleotides happens at the active site.

RNAP contains metal bound to Asp481, 483 and 485. The association of the metal with the bond is between the end of the RNA and the first base. A second metal atom is found at Arg446 (Rpb1) and His1097 and Gln481 of Rpb2 and could associate with -1, -3 and -5 of the RNA hydroxyl groups. Within the bridge helix, which is straight in RANP and bent in Bpol, residues Thr831 and Ala 832 form non-specific contacts with a nucleotide in position +1. Once the bridge helix encounters a nucleotide in +1 it will become straight, and translocation of the base into -1 would result. Movement back without the base would leave a hole in +1 allowing a second base to reside. In order for a phosphodiester bond to form between the RNA bases they must be translocated into -1 and -2 positions and held by protein RNA contacts. Occasionally the base slips out and the abortive cycling process results. At -4 the RNA is exposed meaning no protein contact except for the hydrogen bond at -5. Arg497 Rpb2 (Arg527 in (7) can make electro static interactions with -4 helping to stabilize the abortive transcripts. These abortive transcripts arise when the single stranded RNA and DNA are trapped by the mentioned clamp loops. When RNA of nine or ten residues are present they clash with the TFIIBn domain, which also happens to occupy the saddle region. This clashing allows time to form the strand-loop complex. The three loops that protrude from the clamp, the lid, rudder and loop1 are involved in the separation of the hybrid. In Kornberg's 2004 contribution the details of the lid rudder and the loop are worked out.

The previously mentioned loops lie near the RNAP saddle between the clamp and the wall. The lid forms an arch over the saddle, RNA exits trough the exit pore under the arch and DNA exits above the arch. The lid (Rpb1 246-264) serves as a wedge to drive the hybrid apart at -8,-9 and -10 on the RNA. Phe252 at -10 serves in this function, contacting the plane of its own aromatic ring parallel to the plane of the base. Phe264 acts similar on -10 or -11. The rudder is not directly involved in separation but interacts with the DNA at -9, -10 and -11, preventing the re-association of the RNA-DNA hybrid. Rbp1 Ser318 and Arg320 contact the sugar and the 5( phosphate at position -10. (In Bpol the rudder interacts and accounts for the crosslinking of RNA-DNA hybrid at -7 and -8.) From Rpb2, fork loop1 projects and interacts within the hybrid region on RNA at -5, -6 and -7 attributed to residues Lys471 and Arg476 which interact with the phosphates. Fork loop1 acts to limit strand separation and prevent the unwinding of the hybrid past -8. Resolution of these interactions results in the displacement of TFIIB, which in release of this unit gives rise to promoter escape, and essentially abortive initiation. Once the enzyme has moved past the scaffold complex and re-association of the RNAP the step into elongation can occur.

Stepping into productive elongation is not a default mode, but rather a chosen regulation of gene expression. Positive elongation transcription factors are needed to move from initiation into elongation. TFIIH is dissociated from the enzyme by the conformational change that the nine to ten base RNA DNA hybrid has formed. A factor P-TEFb is needed for the phosphoylation and activated elongation of the RNAP. (11) factor P-TEFa and factor 2 are also needed for stimulation of this step but do not have action in activation of the RNAP. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100A(. Two essential acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is found to be activated by RNAP's weak RNA nuclease capability. The RNA polymerase II CTD is composed of tandem repeated copies of a consensus [YSPTSPS]. P-TEFb is a CTD kinase composed of Cdk9 that carries out Ser2 and 5 phosphorylation of the RNAP's C-Terminal Domain. Elongation can be broken down into steps: the selection of a riobonucleic acid complementary to the template DNA strand; formation of the phosphodietser bond; translocation of the RNA DNA hybrid; separation of the RNA DNA hybrid and reformation of the DNA helix.

Nucleotides enter the holo-enzyme through a channel that leads right the active site. Selection of the base as it enters the active site occurs on the bases of interactions between the protein, RNA and the DNA template. If the base does not match it will not come in contact with the 3( OH group of the RNA due to hindrances in the interactions. The residues Asp485, 483, 481, 836 all line the active site and stabilize one magnesium ion. The active site contains two magnesium metal ions (A and B) that facilitate the rotations of the bases into position for phosphodiester bonding. D837 coordinates the B ion. N479 is thought to be a discriminator of NTP and dNTP molecules. Hindrance does not allow the base to interact with the stationary metal ion A, which is necessary for the rotation into p-bonding distance. Residues K987, 752 and 776, Y769, R1020 and 766 help facilitate the entry and bonding of the base. Elongation pauses from time to time and TFIIS by hydrolytic cleavage of a water molecule in the active site creates new 3( ends to further the bonding interactions. This process proceeds until the transcribing region has reached an end.

Termination in bacteria is facilitated by a Rho dependant or a Rho independent method. Rho is a protein that binds to the transcribed RNA sequence. It hydrolyzes ATP to move towards the RNAP as it is transcribing. Rho begins to wind the RNA around inside itself and slowly catches up to RNAP. The winding action pulls on the RNA and causes stress in the active site as Rho approaches. Near the end of the DNA gene region there are repeat sequences that cause a weaken binding affinity in the active site. Coupled with the stress from Rho and weakened binding affinity the holo-enzyme dissociates. In rho-independent termination the repeated sequences at the end of the transcript have a rich G and C region followed by a poly A or U section. The transcript binds in the G/C repeats forming a secondary hairpin structure, and the poly A or U section leads to the weakened binding affinity in the RNAP. The tension of the structure coupled with weakened binding affinity causes the polymerase to release the transcript. The formation of the loop hairpin can block Rho from reaching the RNAP however termination through either method is inevitable. In eukaryotes there are no strong termination promoter sequences. The RNAP will continue to transcribe until it literally falls off. There is a repeated sequence of Adenine residues added to the transcript, slippage in the reading causes the enzyme to dissociate and fall off the DNA releasing the RNA for post transcriptional modifications.