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Transcription (biology)

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Christian Klar (klar94@web.de) (26/12/2018)


Entry done as an activity of the course: A General Understanding of Information, held in Munich University of Applied Sciences

Transcription is the process in which one of the DNA double-strand is sythesized. (see 2. of Genetic information to understand the structure of DNA) The copy is called RNA and used in the further step called Translation.

N.L.: If you make an enumeration as the following one you should not use epigraphs as you did in your original formatting. I have changed the formatting, not the content.

These are the steps of transcription:

1)  Initiation: In the initiation phase, on one or more small parts of the DNA-double strings, a little bubble(RNA polymerase) wraps arround and travels along the DNA. In those bubbles the double-string complex is first split. Then the bubble travels further it decides for one of the two single strings, reading the information it contains. When read it creates a counter part string(RNA) that is a copy of the string without a bubble arround it. ]

 Transcription begins with the binding of RNA polymerase (RNAP), together with one or more general transcription factors, to a specific DNA sequence, referred to as "promoter". A RNA polymerase-promoter ("closed complex") is now formed. In the "closed complex" the promoter DNA is still fully double-stranded.

The RNAP, assisted by one or more general transcription factors, create a small room where the two strands from the DNA are separated by cutting approximately 14 hydrogen bonds between the oppositional base pairs of the strands to form an “open complex”. The oppositional base pairing system is further explained in paragraph 2. of the article Genetic Information. One strand(strand1) is now separated out of this small room, while the other strand(strand2) is remains in it.

Now a side is selected where the transcription begins. The small room reacts to an initiating nucleoside triphosphate and an extending nucleoside triphosphate, complementary to the transcription start site sequence, and catalyses bond formation to yield an initial RNA product. Transcription initiation is regulated by additional proteins, known as activators and repressors, which modulate formation and function of the transcription initiation complex.

2)  Promoter escape[ At a certain point the synthestzed sting on the DNA string has to esccape it. This process is called promoter escape. After the RNA has left the original string, the bubble(RNA polymerase) travels along and the devided DNA strings assemble again ]

After the first bond is synthesized, the RNA polymerase must escape the promoter. Promoter escape occurs through DNA scrunching, providing the energy needed to break interactions between RNA polymerase holoenzyme and the promoter.

3) Elongation: [  As the bubble(RNA polymerase) travels along the DNA string, it goes on doing its job, reading and sythesizing it. The part of the RNA string that is split off, can already be used as a template for synthesizing a string. Therefore another bubble(RNA polymerase) is needed as in step 2) where the process begins. ]

One strand (strand2) is now further used as a template for RNA synthesis. As transcription proceeds, RNA polymerase traverses the template strand (strand2) and uses base pairing complementarity with the DNA template to create an RNA copy. The complementary bases are bound to strand2. RNA sugar-phosphate backbone forms, with assistance from the polymerase. A complete copy of strand1 is created, called RNA. It can also be used as template for the transcription process as shown in step two (there with strand2). The only difference by using it instead of strand2 would be the sequence of the strands bases. As it would be a copy of strand2, instead of strand1.

process of Elongation

Elongation also involves a proofreading mechanism that can replace incorrectly incorporated bases. In eukaryotes, this may correspond with short pauses during transcription that allow appropriate RNA editing factors to bind. These pauses may be intrinsic to the RNA polymerase or due to chromatin structure.

4) Termination: [ In Termination, as the name implies, the synthesizing process by the bubble(RNA polymerase) needs to be stopped. This is mainly caused by a certain combination of different connections between the DNA strands. This causes the same steps as in 2). ]

Bacteria use two different strategies to stop the transcription process. Rho-Independent strategy and Rho dependent strategy. 

In the Rho-Independent strategy, RNA transcription stops when the newly synthesized RNA molecule forms a G-C-rich hairpin loop followed by a run of Us. When the hairpin forms, the mechanical stress breaks the weak rU-dA bonds, now filling the DNA–RNA hybrid. This pulls the poly-U transcript out of the active site of the RNA polymerase, terminating transcription.

In the "Rho-dependent" type of termination, a protein factor called "Rho" destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex.

Hydrogen bonds between the RNA-DNA helix break, freeing the newly synthesized RNA strand.

If the cell has a nucleus, the RNA may be further processed. This may include polyadenylation, capping, and splicing.

The RNA may remain in the nucleus of exit to the cytoplasm through the nuclear pore complex.

The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. If the gene encodes a protein, the transcription produces messenger RNA (mRNA). Alternatively, the transcribed gene may encode for either non-coding RNA (such as microRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), or other enzymatic RNA molecules called ribozymes.

The mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription. A proofreading mechanism that can replace incorrectly incorporated bases is also applied during the process. In eukaryotes, this may correspond with short pauses during transcription that allow appropriate RNA editing factors to bind. These pauses may be intrinsic to the RNA polymerase or due to chromatin structure.

Different types of RNA (explained in Translation)

DNA scrunching

A process in which RNA polymerase remains stationary while it unwinds and pulls downstream DNA into the transcription complex to pass the nucleotides through the polymerase active site, thereby transcribing the DNA without moving. This causes the unwound DNA to accumulate within the enzyme. RNA polymerase re-winds and ejects the downstream portion of the unwound DNA, releasing the RNA, and reverting to the RNA polymerase-promoter open complex.

Nucleoside triphosphates

Nucleoside triphosphates are molecules used as the building blocks of both DNA and RNA.

Transcription factors

Transcription factors are proteins that combine with the DNA, and control the amount of gene expression that is running, by supporting or slowing the transcription process.

Polyadenylation

Polyadenylation is the addition of a poly(A) tail to a messenger RNA. The poly(A) tail is a stretch of RNA that has only adenine bases. In eukaryotes, polyadenylation is part of the process that matures messenger RNA for translation. The process of polyadenylation begins as the transcription of a gene terminates.

Capping

RNA capping is the process giving the single stranded RNA a defined end. This end is referred to as five-prime cap (5’ cap), due to the placing of it at the beginning of the synthesized RNA strand. It is highly regulated and vital in the creation of stable and mature messenger RNA able to undergo translation during protein synthesis.

Splicing

Splicing is the editing of the nascent precursor messenger RNA transcript into a mature messenger RNA (mRNA). After splicing, introns are removed and exons are joined together. For those eukaryotic genes that contain introns, splicing is usually required in order to create an mRNA molecule that can be translated into protein. For many eukaryotic introns, splicing is carried out in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins.


Overall, RNA helps synthesize, regulate, and process proteins; it therefore plays a fundamental role in performing functions within a cell.



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