to produce a functional RNA molecule the cell must make an RNA copy of a DNA sequence in double stranded DNA The Strand to be copied is known as the coding strand the other strand which contains the compliment base sequence is the template strand that will be used to form the RNA transcript so what are the key features of the coding strand the start of the coding sequence is known as the transcription start site to the five Prime side of this site is the promoter region the promoter region contains particular DNA sites known as core promoter elements these are important in the Assembly of the complex of proteins that are needed to initiate transcription this complex is called the transcription initiation complex and contains the RNA polymerase 2 enzyme along with additional proteins or protein complexes known as transcription factors transcription factors help RNA poas to locate the promoter and ini initiate transcription we'll now consider how the initiation complex assembles the first step in the Assembly of the transcription initiation complex is The Binding of the transcription factor tf2d to the tataa box which is one of the core DNA promoter elements tf2d is a complex of proteins and contains the key subunit that binds the Tata box this key subunit is known as Tata binding protein or tbp the TB PP subunit induces profound bending of the DNA binding of tf2d is followed by The Binding of tf2a and tf2b tf2b binds the core promoter element called the BR as well as contacting tf2d in The Next Step the RNA polymerase 2 core enzyme is recruited together with TF2 F finally TF2 e and tf2h are recruited to form the complete transcription initiation complex this is the closed complex meaning that the DNA is still double stranded and the template strand has not yet been exposed transcription begins with a separation of the two DNA strands to form the open complex this separation depends on tf2h which uses energy from ATP hydrolysis to unwind the DNA and promote strand opening the short stretch of DNA with unpaired strands is called a transcription bubble the opening of the transcription bubble exposes the template strand which will be used to form a complimentary RNA strand free ribonucleoside triphosphates enter through the funnel region of the RNA polymerase and form base pairing interactions with the template strand RNA polymerase catalyzes the addition of nucleotides to the three prime hydroxy of the last base in the growing chain this means that the RNA grows in the five Prime to three prime Direction transcription initiation does not go smoothly RNA polymerase typically will start to synthesize the RNA but the RNA product will diffuse away after it has reached a length of just a few base pairs the whole process of synthesis then starts again this process is known as abortive initiation after multiple rounds of abortive initiation RNA polymerases breaks free of the promoter and continues to synthesize the RNA in a more persistent way this phase is called promoter clearance RNA polymerase now forms a stable complex with the DNA continues to synthesize the RNA at the same time tf2h phosphates the C terminal domain of the large subunits of RNA polymerase 2 this domain is called ctd this phosphorilation of ctd is key to the processing of the RNA to produce the mature transcript and this is what happens next during the RNA processing step a complex of RNA processing enzymes called ptefb binds the phosphorated ctd as the five Prime end of the growing RNA comes out to the exit channel of RNA polymerase ptefb cently attaches a guanosine cap to the five Prime end of the RNA ptfb then attaches additional phosphate groups to the ctd which causes transcription elongation which is paused to resume the more highly phosphorated ctd also can recruit additional RNA processing enzymes that will be needed to complete processing of the transcript at the end of the transcription cycle RNA polymerase is now transitioned into the elongation phase during this phase the growing RNA strand comes out of the RNA polymerase exit Channel as it continues to elongate transcription bubble moves along with the RNA polymerase DNA base pairs are separated ahead of the transcribing pimas to expose more of the template strand while bases in the wake of the pimas reanneal in this way RNA pimas can continue until it has transcribed the complete RNA RNA polymerase doesn't always make it to the end of the coding sequence in one smooth Journey instead RNA polymerase can sometimes stall before reaching the end of the transcribed region the perim ray can be restarted by The Binding of elongation factors but sometimes the RNA Pim raay starts to backtrack this means that the Pim raas slides backwards along with the transcription bule this causes the three prime end of the growing transcript to become unpaired and to come out through the funnel region of the RNA polymerase the transcription Factor tf2s can rescue the stall polymerase by binding in the funnel region and promoting cleavage of a three prime end of the RNA that is unpaired this exposes a new thre Prime hydroxy in the RNA that is correctly positioned in the active site transcription can now resume as before transcription continues until RNA polymerase 2 reaches a sequence in the DNA called a polyadenylation signal after RNA polymerases is transcribed through this signal sequences in the RNA transcript associate with the RNA processing proteins that abound to the polymerase ctd these proteins cleave the RNA transcript and add a sequence of adenine nucleo TI to the three prime end of the transcript this run of adenines is called a po a tail once the polya tail is added RNA polymerase dissociates from the DNA and mature RNA is released at this point transcription is terminated and an RNA transcript has been successfully produced