Transcription Pt II

Transcription in eukaryotes is undertaken by polymerses closely related to the polymerases  found in prokaryotes. However, there are differences in the machinery used in each case name two

RNA polymerase II core promoters are made up of combinations of ________ classes of sequence element

The eukaryotic ______ ______ refers to the minimal set of sequence elements required for accurate transcription initiation by the Pol II machinery used in vitro

A core promoter is typically ______ nucleotides long, extending either ______ or _____ from the transcription start site.

Elements found in Pol II core promoters (relative to the transcription start site) (4)

Typically, a promoter includes some subset of those four elements. State an example

The _____ is the most common element , found in combination with both TATA and DPEs.

RNA polymerase II forms a _______ complex with GTFs at the promoter

The ______ collectively perform the functions perform function of σ in bacterial transcription. So they help polymerase bind to the _____ and ______ the DNA. They also help polymerase ______ the promoter and embark on the _______ phase

preinitation complex

Many pol II promoters contain a ______ element found 30bp _______ from the transcription start site.

The TATA element is recognized by the GTF called ______. The nomenclature _____ denotes a transcription factor for Pol II. Like many of the GTFs, it is a _____ _____ complex

The component of TFIID that binds to the TATA DNA sequence is called ______ _____ ______. The other subunits in this complex are called ______ ______ ______.

Some TAFs recognize other core promoter elements such as _____, ______ and _____ although the strongest binding is between _____ and _______. Thus TFIID is a critical factor in _______ recognition and _______ complex establishment

Upon binding DNA, TBP extensively ______ the TATA sequence. The resulting TBP-DNA complex provides a platform to ______ other GTFs and polymerases to the promote.

The order the proteins assemble at the promoter (in vitro)

Formation of the preintiation complex containing these components is followed by ______ _______. In contrast to bacteria, in eukaryotes this action requires ____ _______ and is mediated by ______

Promoter escape requires __________ of the polymerase tail

Before the polymerase escapes the promoter and enters the elongation phase, there is a period of _______ initiation

abortive initiation

In eukaryotes, promoter escape involves two steps, name them

TBP is associated with about ____ TAFs. Two of the TAFs bind DNA elements (Inr and downstream ______ elements) at the ______.

TFIIB is a protein is a single _______ _____. It enters the preinitaiton complex after _______.

TFIIF has _____  subunits in humans and associates with ______. It is recruited to the promoter with _______.

Binding of ______ to ______stabilizes the DNA-TBP-TFIIB complex and is required before _____ and _____ are recruited to the preinitiation complex

TFIIE consists of _____ subunits, binds after ______. It has roles in ______ and ______ of TFIIH. TFIIH controls the ____ dependent transition of the preinitiation complex to the open complex. TFIIH is also the _______ and ______ complicated of the GTFs. It has _____ subunits and a molecular mass comparable to the ______ itself.

Within TFIIH are two subunits that function as ______ (involved in ______ excision repair) and another that is a ______ ______, with roles in promoter melting and escape

In bacteria, melting of the 10 element promoter is mediated by bases on the _______ DNA strand being _______ out and bound within pockets in the σ subunit. This ______ (does/doesn't) require ATP hydryolysis and is driven simply by _____ reactions that favor the _______ conformation

In eukaryotes the TFIIH acts as an ATP-driven _______ of double stranded DNA. This subunit binds to DNA _____ from the polymerase and feeds _____ _____ DNA with right handed threading, into the ______ of the polymerase. This action drives the _____ of the DNA because the upstream promoter DNA is held in a ______ position by ______ and the rest of the _____.

Elongating polymerase is associated with a new set of protein factors required for various types of RNA ______

Once transcribed, eukaryotic RNA has to be processed in various ways before being _______ from the nucleus where it can be _______. Name the three processing events

The most complicated of the processing events is _______. It is a process where ________ ________ are removed from RNA to generate the mature mRNA.

There is an overlap in _______ involved in elongation and those required for RNA processing. In one 5 also helps to case, an elongation factor SPT5 also helps to recruit the ______ enzyme to the CTD tail of polymerase. Where is it phosphorylated?

In another case, elongation factor TAT-SF1 recruits components of the splicing machinery to polymerase with with a Ser-2 ________ tail. Thus _______, _______ of transcription and RNA _______ are interconnected, to ensure their proper coordination

The first RNA processing event is _______. This involves the addition of a modified _______ base to the to the _____ of the RNA. Specifically, the base added is ______ ______, and it is joined to the RNA transcript by an unusual ______ linkage involving _____ phosphates

The 5' cap is created in three enzymatic steps (mini story: 3)

The RNA is capped as soon as it emerges from the _____ _____ _______ of polymerase. This happens when the transcription cycle has progressed only as far as the transition from the ______ to _____ phases.

After capping, _________ of Ser-5 within the tail repeats may be responsible for dissociation of the capping machinery, and further ________ (of Ser-2 within the ____ _____) causes recruitment of the machinery needed ____ ______.

The final RNA processing event is _________ of the 3' end of the mRNA . It is intimately linked with the _______ of transcription. Just as with capping splicing, the polymerase CTD tail is involved in recruiting some of the enzymes necessary for _________.

Once polymerase has reached the end of the a gene, it encounters specific _______ that, after being ________ into RNA, trigger the transfer of ________ enzymes to that RNA, leading to four events. Name them

Which two protein complexes are carried by the CTD of polymerase as it approaches the end of the gene

The sequences that, once transcribed into RNA, trigger transfer of CPSF and CSTF to the RNA are called _____ _______. Once CPSF and CSTF are bound to the RNA, other proteins are recruited as well, leading initially to RNA _______ and then ________.

Polyadenylation is mediated by an enzyme called _____ ________, and it adds approx. _____ adenines to the RNA's ______ produced by the cleavage.

Poly-A polymerase uses _____ as a precursor and adds nucleotides using the same chemistry as RNA polymerase. However, it does so without a _______. Thus, the long tail of As is found in the _____ but not in the _____.

What terminates transcription by polymerase? **

Transcription termination is linked to RNA destruction by a highly ______ _____

Polyadenylation is linked to termination, although it is unclear how. An enzyme that ______ the second RNA as it emerges from the polymerase has been identified, and this enzyme may itself trigger _______. This is called the _______ model

According to the torpedo model, the free end of the second RNA is ______ and thus can be distinguished from genuine transcripts. This new RNA is recognized by an ______ called

The RNase in the torpedo model is called _____ in yeasts and _____ in humans. It is loaded onto the end of the RNA by another protein (Rtt103) that binds the _____ of RNA polymerase.

Rat1 enzyme is very _______ and quickly degrades the RNA in a _______ direction, until it catches up to the ________ polymerase from which the RNA is being spewed. Termination may not require any specific interaction between ____ and the polymerase. It may be triggered in a manner rather similar to _____ _______ termination in bacteria

Although the torpedo model for termination is now the favored one, there is an alternative called the _______ model. According to this model, termination depends on a _________ change in the elongating polymerase that reduces the ________ of the enzyme leading to spontaneous termination soon afterward. The _________ change would be linked to polyadenylation and could, for example, be triggered by the transfer of 3'-processing enzymes from the _____ _____ of polymerase to the RNA or by binding of the ____ _____ of other factors that induce a _______ change.

RNA pol I and pol III make _______ RNAs