Transcription

Transcription is, ______ and ______, very similar to DNA replication. Both involve enzymes. Both involve enzymes that synthesize a new strand of nucleic acids complementary to a _____ _____ strand.

Name four differences between transcription and DNA replication

The RNA product does not remain base-paired to the DNA template strand. Meaning?

The discplacement of the growing chain a few nucleotides behind where each ribonucleotide is added critical for the ____ to perform its functions. Furthermore, because this release follows so closely behind the site of polymerization, multiple ____ ______ can transcribe the same gene at the same time, each following closely behind the other

As an RNA product dissociates from the DNA template just behind each advancing RNA polymerase, the two DNA strands _______

The difference in precision between transcription and replication reflects the lac of extensive _______ mechanisms for transcription, although ______ forms of ________ exist for RNA synthesis

It makes sense for the cell to worry more about the ________ of the replication than that of transcription. DNA is a molecule in which the genetic material is ______, and DNA replication is the process by which that genetic material is passed on. Any mistake that arises during ______ can easily be catastrophic: it becomes _______ in the genome of the individual and gets passed on to subsequent generations

Transcription, in contrast to replication, produces only _____ _____ and normally several from each transcribed region. Thus, a mistake during transcription will rarely do more harm than render one out of many _____ ______ defective

Transciprion only selectively copies certain parts of the _______ and makes anywhere 100 - 1000s of copies of any given section. In contrast, replication must copy the entire ______ and do so ______ every cell division.

RNA polymerases perform essentially the ______ reactions in all cells, from bacteria to humans. It is thus not surprising that the enzymes from these organisms _____ many features. Where specifically?

Bacteria have ______ RNA polymerase, while eukaryotic cells _____. Name them

Pol II is the most ______ of these polymerase enzymes, it is also the polymerase responsible for _______ most genes, particularly all _____ encoding genes.

Pol I and Pol III are each involved in transcribing specialized _____ encoding genes. Specifically, Pol I transcribes the large _____  precursor gene, whereas Pol III transcribes ______ genes, some small nuclear RNA genes and the 5SrRNA gene.

The bacterial RNA polymerase _____ _____ alone is capable of synthesizing RNA and comprises two copies of the ____ subunit and one of each of ___, ____ and ____ subunits

The core enzyme is closely related to the eukaryotic polymerases. Name the counterparts for these core enzymes for either Pol I, Pol II or Pol III

The bacterial and yeast enzymes share an overall _____ and _____.  This is more true for the internal parts near the _____ ______ and less so for on the ________. Does this make sense? Why or why not?

Overall, the shape of each enzyme resembles a crab claw, (like the hand of DNA pol). The two _______ of the crab claw are made predominantly of of the two _____ subunits of each enzyme. It is ___ and ____ for prokaryotes and _____ and _____ for eukaryotic enzymes

The active site which is made up of regions from both subunits, is found at he base of the pincers within a region called the ______ _____ ______. The active site works according to the two ____ ____catalytic mechanism for nucleotide addition proposed for all types of polymerases

To transcribe a gene, RNA polymerase proceeds through a series of well defined steps grouped into three phases. Name them

A ______ is the DNA sequence that initially binds the RNA polymerase (together with any initiation factors required) [**in initiation]

Initiation story (6)

When does elongation begin

Elongation story (4)

Once the polymerase has transcribed the length of the gene, it must stop and ______ the RNA product and _______ from the DNA itself, this is called ________. In some cells, specific ______ trigger this, in others it is less clear.

Transcription initiation can be broken down into ______ steps. The first is called _____ complex, the second is called ______ complex and the third is called ______ ______  complex

When an enzyme makes a transcript longer than ____ _______, it is said to have escaped the promoter. At this point, it has formed a stable ternary complex, containing ______, ____ and ____. This is the transition to the ______ phase

The bacterial core RNA polymerase can initiate transcription at any point on a DNA molecule, and this can be shown in vitro using purified _____ _____. However, in cells, polymerase initiates transcription only at _______.

It is the addition of an initiation factor called ____ that converts core enzymes into the form that initiates only at promoters. This form of the enzyme is called the ____ _____ _______.

Promoters recognized by polymerase containing σ share the following characteristic

The two conserved sequences of 6 nucleotides are centered respectively at ____ and at _____ upstream of the site where _____ ______ starts. What are the sequences called?

Transcription is initiated by RNA polymerase without the need for a ______

Why does DNA replication always need a primer strand?

The primer is typically a short piece of ____ that binds to the ____ ______ strand to form a short hybrid double strand region. DNA polymerase then adds nucleotides to the ______ of the primer.

RNA polymerae can initiate a new RNA chain on a DNA template and does not need a primer. Name two things necessary for this feat

Bringing the initiating ribonucleotide to the active site and holding it stably on the template while the next NTP is presented is difficult, why?

The elongating polymerase is a _______ machine that syntesizes and proofreads RNA

DNA passes through the elongating enzyme in a manner similar to its passage through the open complex. Thus, double stranded DNA enters the ____ of the enzyme between the ______.

At the opening of the ______ ______, the strands separate to follow different paths through the elongating enzyme before exiting through their respective ______ and re-forming a ____ _____ behind the elongating polymerase.

Ribonucleotides enter the _____ _____ of the elongating polymerase through their defined channel and are added to the growing _____ chain under the guidance of the _____ ______ strand.

Only 8 or 9 nucleotides of growing RNA chain remain base-paired to the _____ ______ at any given time; the remainder of the RNA chain is ______ ______ and directed out of the enzyme through the RNA ______ _______

During elongation, the elongation enzyme adds _____ nucleotide at a time to grow the RNA transcript. Elongation polymerase acts as a molecular _____, advancing in a single step a distance equivalent to a base pair for every _______ it adds to the growing RNA chain. In addition, the size of the bubble (the length of DNA that is not _____ stranded), is ______ throughout elongation. Explain

While synthesizing the transcript, RNA polymerase performs two proofreading functions on that growing transcript, name them

In pyrophosphorolytic editing, the enzyme uses its ______ _____ in a simple back-reaction, to catalyze the removal of an incorrectly inserted ________, by reincorporation of _____. The enzyme can then incorporate another _______ in its place in the growing RNA chain.

In pyrophosphorolytic editing the enzyme can remove either ______ or ______ bases but spends longer hovering over _______ than _____ making it more accurate. How many nucleotides does it backtrack by?

In hydrolytic editing, the polymerase _______ by one or more nucleotides and ______ the RNA product, removing the ______ containing sequence

Hydrolytic editing is stimulated by _____ _____, which both _______ hydrolytic editing function and serve as elongation stimulation factors. Explain

Another group of proteins the ______ proteins join polymerase in the elongation phase and promotes the process of _______ and _______. These proteins are most similar to _____

Gre factors are equivalent to?

Under certain circumstances, an elongating RNA pol can become _______ and cease transcribing. One common cause is a ________ DNA strand.

The consequences of arrest if the gene is being transcribed

To deal with arrest, the cell has machinery that removes the ______ and at the same time recruits repair enzymes called ______. The repair process is called _____ _____ repair and the protein that does both repair and removal is called ______

Transcription is terminated by signals within the _____ ______

When RNA polymerase arrests during _______, it can be knocked off DNA by the action of the translocator ________. This termination is triggered by _______ DNA or by other unanticipated hindrances.

Where is termination a normal and important function

At the ends of genes, sequences called ______ trigger the elongating polymerase to dissociate from the DNA and release the _____ _____ it has made.

Two types of terminators in bacteria

Rho-dependent terminators require a protein called _____ to induce _______. The second cause Rho-independent causes _______ without the involvement of other factors

Rho:
rut sites:

Rho dependent terminator story:

How is rho directed to work on particular RNA transcripts?

Rho-independent terminators, also called _______ __________ because they need no other factors to work, consist of two sequence elements, name them

The elements of intrinsic terminators do not affect the polymerase unitl they have been ______. Meaning?

When polymerase transcribes an inverted repeat sequence, the resulting RNA can form a _____ _____ structure aka ______ by base pairing itself. How does this cause termination