What is the benefit of the coding strand if it doesn't get transcribed and only the template strand gets transcribed? Please answer asap. Thank you!

Having 2 strands is essential in the DNA replication process, where both strands act as a template in creating a copy of the DNA and repairing damage to the DNA. Additionally the process of transcription is directional with the coding strand acting as the template strand for genes that are being transcribed the other way. In the diagrams used in this article the RNA polymerase is moving from left to right with the bottom strand of DNA as the template. If the promoter orientated the RNA polymerase to go in the other direction, right to left, because it must move along the template from 3' to 5' then the top DNA strand would be the template.

During DNA replication ,DNA ligase enzyme is used alongwith DNA polymerase enzyme so during transcription is RNA ligase enzyme also used along with RNA polymerase enzyme to complete the phosphodiester backbone of the mRNA between the gaps?

*Great question*! Not during normal transcription, but in case RNA has to be modified, e.g. bacteriophage, there is T4 RNA ligase (Prokaryotic enzyme). (s the ability of bacteriophage T4 to rescue essential tRNAs nicked by host nucleases, or in the more exotic RNA editing processes seen in kinetoplastids, in which mRNA molecules are cut, their coding sequence altered, and then the RNA pieces spliced back together). Nucleotidyl transferases share the same basic mechanism, which is the case of RNA ligase begins with a molecule of ATP is attacked by a nucleophilic lysine, adenylating the enzyme and releasing pyrophosphate. https://www.cell.com/molecular-cell/pdf/S1097-2765(04)00089-9.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234903/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1624903/

Why does RNA have the base uracil instead of thymine?

To add to the above answer, uracil is also less stable than thymine. RNA molecules are constantly being taken apart and put together in a cell, and the lower stability of uracil makes these processes smoother. In DNA, however, the stability provided by thymine is necessary to prevent mutations and errors in the cell's genetic code. :)

i heard ATP is necessary for transcription. Which process does it go in and where? (initiation, elongation, termination)

ATP is need at point where transcription facters get attached with promoter region of DNA , addition of nucleotides also need energy durring elongation and there is also need of energy when stop codon reached and mRNA deattached from DNA. There for termination reached when poly Adenine region appeared on DNA templet because less energy is required to break two hydrogen bonds rather than three hydrogen bonds of c, G. transcription process starts after a strong signal it will not starts on a weak signals because its energy consuming process.

What about termination in eukaryotes?

Termination in eukaryotes is much more complex and varies depending on the gene and organism. But generally, as mentioned in the article, a polyadenylation signal is released, which attracts rna cleavage proteins (which also varies!) and cuts the mRNA off.

so there are many promoter regions in a DNA, which means how RNA Polymerase know which promoter to start bind with. what triggers particular promoter region to start depending upon situation.

This is a good question, but far too complex to answer here. In fact, this is an area of active research and so a complete answer is still being worked out. There are many known factors that affect whether a gene is transcribed. These include factors that alter the accessibility of chromatin (chromatin remodeling), and factors that more-or-less directly regulate transcription (e.g transcription factors). Also worth noting that there are many copies of the RNA polymerase complex present in each cell — one reference§ suggests that there could be hundreds to thousands of separate transcription reactions occurring simultaneously in a single cell! The following are a couple of other sections of KhanAcademy that provide an introduction to this fascinating area of study: https://www.khanacademy.org/science/biology/gene-regulation https://www.khanacademy.org/test-prep/mcat/biomolecules#gene-control §Reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926752/

Concerning Rho-independent termination, why does the RNA fold back onto itself after reaching the C-G rich region, I get the purpose of the stable bonds formed by C-G nucleotides, but I'm just confused about the folding.

If you had, say, a paper clip, and you stretched it out so the wire was straight, and then hold it by one end and press it into a wall, what would happen? The wire would bend back in on itself because it no longer has anywhere else to go in that direction, but its momentum forces it to go _somewhere_, making it bend in a different direction. I believe that is what occurs when the RNA hits the terminator. I hope this helped! Comment if you have any questions; I'll answer to the best of my ability.

Do promoters and terminators get copied into the new transcript? Are they are part of the new RNA transcript after transcription has ended?

Promoters and terminators do not get copied into the new transcript. The promoter is there to tell the RNA to "get ready" and signal the start of the transcription site. The RNA binds to it, but does not copy it. The same is true of the terminator. It stops the RNA's momentum, letting it know that it needs to stop transcribing. In Rho-dependant reactions, I do not believe the terminator could be copied by the RNA anyway. So the answer to your question is no, the promoters and terminators are not copied. I hope this helped! Comment if you have any questions; I'll answer to the best of my ability.

According to my notes from my biochemistry class, they say that the rho factor binds to the c-rich region in the rho dependent termination, not the independent. Therefore, in order for termination to occur, rho binds to the region which contains helicase activity and unwinds the 3' end of the transcript from the template. However, if I am reading correctly, the article says that rho binds to the C-rich protein in the rho independent termination. I am still a bit confused with what is correct.

The article says that in Rho-independent termination, RNA polymerase stumbles upon rich C region which causes mRNA to fold on itself (to connect C and Gs) creating hairpin. That hairpin makes Polymerase stuck and termination of elongation. I do not see the Rho factor mentioned in the text nor on the photo. Probably those Cs and Gs confused you. :D

Main content

Course: Biology library > Unit 18

Lesson 2: Transcription

Stages of transcription

Google Classroom

An in-depth looks at how transcription works. Initiation (promoters), elongation, and termination.

Key points:

Transcription is the process in which a gene's DNA sequence is copied (transcribed) to make an RNA molecule.
RNA polymerase is the main transcription enzyme.
Transcription begins when RNA polymerase binds to a promoter sequence near the beginning of a gene (directly or through helper proteins).
RNA polymerase uses one of the DNA strands (the template strand) as a template to make a new, complementary RNA molecule.
Transcription ends in a process called termination. Termination depends on sequences in the RNA, which signal that the transcript is finished.

Introduction

What makes death cap mushrooms deadly? These mushrooms get their lethal effects by producing one specific toxin, which attaches to a crucial enzyme in the human body: RNA polymerase.

^{1}

RNA polymerase is crucial because it carries out transcription, the process of copying DNA (deoxyribonucleic acid, the genetic material) into RNA (ribonucleic acid, a similar but more short-lived molecule).

Transcription is an essential step in using the information from genes in our DNA to make proteins. Proteins are the key molecules that give cells structure and keep them running. Blocking transcription with mushroom toxin causes liver failure and death, because no new RNAs—and thus, no new proteins—can be made.

^{2}

Transcription is essential to life, and understanding how it works is important to human health. Let's take a closer look at what happens during transcription.

Transcription overview

Transcription is the first step of gene expression. During this process, the DNA sequence of a gene is copied into RNA.

Before transcription can take place, the DNA double helix must unwind near the gene that is getting transcribed. The region of opened-up DNA is called a transcription bubble.

Transcription uses one of the two exposed DNA strands as a template; this strand is called the template strand. The RNA product is complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate (or coding) strand. However, there is one important difference: in the newly made RNA, all of the T nucleotides are replaced with U nucleotides.

The site on the DNA from which the first RNA nucleotide is transcribed is called the

+ 1

site, or the initiation site. Nucleotides that come before the initiation site are given negative numbers and said to be upstream. Nucleotides that come after the initiation site are marked with positive numbers and said to be downstream.

If the gene that's transcribed encodes a protein (which many genes do), the RNA molecule will be read to make a protein in a process called translation.

RNA polymerase

RNA polymerases are enzymes that transcribe DNA into RNA. Using a DNA template, RNA polymerase builds a new RNA molecule through base pairing. For instance, if there is a G in the DNA template, RNA polymerase will add a C to the new, growing RNA strand.

RNA polymerase always builds a new RNA strand in the 5’ to 3’ direction. That is, it can only add RNA nucleotides (A, U, C, or G) to the 3' end of the strand.

The two ends of a strand of DNA or RNA strand are different from each other. That is, a DNA or RNA strand has directionality.

At the 5’ end of the chain, the phosphate group of the first nucleotide in the chain sticks out. The phosphate group is attached to the 5' carbon of the sugar ring, which is why this is called the 5' end.
At the other end, called the 3’ end, the hydroxyl of the last nucleotide added to the chain is exposed. The hydroxyl group is attached to the 3' carbon of the sugar ring, which is why this is called the 3' end.

Many processes, such as DNA replication and transcription, can only take place in one particular direction relative the the directionality of a DNA or RNA strand.

You can learn more in the article on nucleic acids.

RNA polymerases are large enzymes with multiple subunits, even in simple organisms like bacteria. Humans and other eukaryotes have three different kinds of RNA polymerase: I, II, and III. Each one specializes in transcribing certain classes of genes. Plants have an additional two kinds of RNA polymerase, IV and V, which are involved in the synthesis of certain small RNAs.

Transcription initiation

To begin transcribing a gene, RNA polymerase binds to the DNA of the gene at a region called the promoter. Basically, the promoter tells the polymerase where to "sit down" on the DNA and begin transcribing.

Each gene (or, in bacteria, each group of genes transcribed together) has its own promoter. A promoter contains DNA sequences that let RNA polymerase or its helper proteins attach to the DNA. Once the transcription bubble has formed, the polymerase can start transcribing.

Promoters in bacteria

To get a better sense of how a promoter works, let's look an example from bacteria. A typical bacterial promoter contains two important DNA sequences, the $-$ ‍ $10$ ‍ and $-$ ‍ $35$ ‍ elements.

RNA polymerase recognizes and binds directly to these sequences. The sequences position the polymerase in the right spot to start transcribing a target gene, and they also make sure it's pointing in the right direction.

Once the RNA polymerase has bound, it can open up the DNA and get to work. DNA opening occurs at the

-

10

element, where the strands are easy to separate due to the many As and Ts (which bind to each other using just two hydrogen bonds, rather than the three hydrogen bonds of Gs and Cs).

The

-

10

and the

-

35

elements get their names because they come

35

and

10

nucleotides before the initiation site (

+ 1

in the DNA). The minus signs just mean that they are before, not after, the initiation site.

Promoters in humans

In eukaryotes like humans, the main RNA polymerase in your cells does not attach directly to promoters like bacterial RNA polymerase. Instead, helper proteins called basal (general) transcription factors bind to the promoter first, helping the RNA polymerase in your cells get a foothold on the DNA.

Many eukaryotic promoters have a sequence called a TATA box. The TATA box plays a role much like that of the

-

10

element in bacteria. It's recognized by one of the general transcription factors, allowing other transcription factors and eventually RNA polymerase to bind. It also contains lots of As and Ts, which make it easy to pull the strands of DNA apart.

Elongation

Once RNA polymerase is in position at the promoter, the next step of transcription—elongation—can begin. Basically, elongation is the stage when the RNA strand gets longer, thanks to the addition of new nucleotides.

During elongation, RNA polymerase "walks" along one strand of DNA, known as the template strand, in the 3' to 5' direction. For each nucleotide in the template, RNA polymerase adds a matching (complementary) RNA nucleotide to the 3' end of the RNA strand.

The RNA transcript is nearly identical to the non-template, or coding, strand of DNA. However, RNA strands have the base uracil (U) in place of thymine (T), as well as a slightly different sugar in the nucleotide. So, as we can see in the diagram above, each T of the coding strand is replaced with a U in the RNA transcript.

RNA nucleotides are similar to DNA nucleotides, but not identical. They have a ribose sugar rather than deoxyribose, so they have a hydroxyl group on the 2' carbon of the sugar ring. Also, in RNA, there is no T (thymine). Instead, RNA nucleotides carry the base uracil (U), which is structurally similar to thymine and forms complementary base pairs with adenine (A).

The picture below shows DNA being transcribed by many RNA polymerases at the same time, each with an RNA "tail" trailing behind it. The polymerases near the start of the gene have short RNA tails, which get longer and longer as the polymerase transcribes more of the gene.

Transcription termination

RNA polymerase will keep transcribing until it gets signals to stop. The process of ending transcription is called termination, and it happens once the polymerase transcribes a sequence of DNA known as a terminator.

Termination in bacteria

There are two major termination strategies found in bacteria: Rho-dependent and Rho-independent.

In Rho-dependent termination, the RNA contains a binding site for a protein called Rho factor. Rho factor binds to this sequence and starts "climbing" up the transcript towards RNA polymerase.

When it catches up with the polymerase at the transcription bubble, Rho pulls the RNA transcript and the template DNA strand apart, releasing the RNA molecule and ending transcription. Another sequence found later in the DNA, called the transcription stop point, causes RNA polymerase to pause and thus helps Rho catch up.

^{4}

Rho-independent termination depends on specific sequences in the DNA template strand. As the RNA polymerase approaches the end of the gene being transcribed, it hits a region rich in C and G nucleotides. The RNA transcribed from this region folds back on itself, and the complementary C and G nucleotides bind together. The result is a stable hairpin that causes the polymerase to stall.

In a terminator, the hairpin is followed by a stretch of U nucleotides in the RNA, which match up with A nucleotides in the template DNA. The complementary U-A region of the RNA transcript forms only a weak interaction with the template DNA. This, coupled with the stalled polymerase, produces enough instability for the enzyme to fall off and liberate the new RNA transcript.

In eukaryotes like humans, transcription termination happens differently depending on the type of gene involved. Here, we'll see how termination works for protein-coding genes.

Note: This is a pretty weird mechanism. It does not make complete sense, even to the biologists who study it in great detail. You have been warned!

Termination begins when a polyadenylation signal appears in the RNA transcript. This is a sequence of nucleotides that marks where an RNA transcript should end. The polyadenylation signal is recognized by an enzyme that cuts the RNA transcript nearby, releasing it from RNA polymerase.

Oddly enough, RNA polymerase continues transcribing after the transcript is released, often making

500

-

2,

000

more nucleotides' worth of RNA

^{5}

. Eventually, it detaches from the DNA through mechanisms that are not yet fully understood

^{6}

. The extra RNA is not usually translated and seems to be a wasteful byproduct of transcription.

What happens to the RNA transcript?

After termination, transcription is finished. An RNA transcript that is ready to be used in translation is called a messenger RNA (mRNA). In bacteria, RNA transcripts are ready to be translated right after transcription. In fact, they're actually ready a little sooner than that: translation may start while transcription is still going on!

In the diagram below, mRNAs are being transcribed from several different genes. Although transcription is still in progress, ribosomes have attached each mRNA and begun to translate it into protein. When an mRNA is being translated by multiple ribosomes, the mRNA and ribosomes together are said to form a polyribosome.

Why can transcription and translation happen simultaneously for an mRNA in bacteria? One reason is that these processes occur in the same 5' to 3' direction. That means one can follow or "chase" another that's still occurring. Also, in bacteria, there are no internal membrane compartments to separate transcription from translation.

The picture is different in the cells of humans and other eukaryotes. That's because transcription happens in the nucleus of human cells, while translation happens in the cytosol. Also, in eukaryotes, RNA molecules need to go through special processing steps before translation. That means translation can't start until transcription and RNA processing are fully finished. You can learn more about these steps in the transcription and RNA processing video.

Attribution:

This article is a modified derivative of the following articles:

"Prokaryotic transcription," by OpenStax College, Biology, CC BY 4.0. Download the original article for free at http://cnx.org/contents/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.61.
- "Eukaryotic transcription," by OpenStax College, Biology, CC BY 4.0. Download the original article for free at http://cnx.org/contents/185cbf87-c72e-48f5-b51e-f14f21b5eabd@10.61.

The modified article is licensed under a CC BY-NC-SA 4.0 license.

Works cited:

Berger, S. (2006). The mushroom Amanita phalloides. In Transcription and RNA polymerase II. Retrieved from http://www.chem.uwec.edu/Webpapers2006/sites/bergersl/pages/amanitin.html.
Amanita phalloides. (2016, February 6). Retrieved February 13, 2016 from Wikipedia: https://en.wikipedia.org/wiki/Amanita_phalloides.
CyberBridge. (2007). RNA structure. In Structure of DNA. Retrieved from http://cyberbridge.mcb.harvard.edu/dna_3.html.
Rho factor. (2016, October 19). Retrieved November 20, 2016 from Wikipedia: https://en.wikipedia.org/wiki/Rho_factor.
Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., and Darnell, J. (2000). Three eukaryotic RNA polymerases employ different termination mechanisms. n Molecular cell biology (4th ed., section 11.1). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK21601/#_A2857_.
Richard, P. and Manley, J. L. (2009). Transcription termination by nuclear RNA polymerases. Genes & Dev., 23, 1247-1269. http://genesdev.cshlp.org/content/23/11/1247.full.

References:

3'-end cleavage and polyadenylation. (2016). In Nobelprize.org. Retrieved from http://www.nobelprize.org/educational/medicine/dna/a/splicing/splicing_endformation.html.

Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., and Walter, P. (2002). Posttranscriptional controls. In Molecular biology of the cell (4th ed.). New York, NY: Garland Science. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK26890/.

Alpha-amanitin. (2016, February 11). Retrieved February 13, 2016 from Wikipedia: https://en.wikipedia.org/wiki/Alpha-Amanitin.

Amanita phalloides. (2016, February 6). Retrieved February 13, 2016 from Wikipedia: https://en.wikipedia.org/wiki/Amanita_phalloides.

Berg, J. M., Tymoczko, J. L., and Stryer, L. (2002). Transcription is catalyzed by RNA polymerase. In Biochemistry (5th ed., section 28.1). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK22546/.

Berger, Shanna. (2006). Eukaryotic transcription. In Transcription and RNA polymerase II. Retrieved from http://www.chem.uwec.edu/Webpapers2006/sites/bergersl/pages/eukaryotic.html.

Berger, S. (2006). The mushroom Amanita phalloides. In Transcription and RNA polymerase II. Retrieved from http://www.chem.uwec.edu/Webpapers2006/sites/bergersl/pages/amanitin.html.

Boundless (2016, January 8). Initiation of transcription in eukaryotes. In Boundless biology. Retrieved from https://www.boundless.com/biology/textbooks/boundless-biology-textbook/genes-and-proteins-15/eukaryotic-transcription-108/initiation-of-transcription-in-eukaryotes-445-11670/.

Brown, T. A. (2002). Assembly of the transcription initiation complex. In Genomes (2nd ed., Ch. 9). Oxford, UK: Wiley-Liss. Retrieved from www.ncbi.nlm.nih.gov/books/NBK21115/.

Gong, X. Q., Nedialkov, Y. A., and Burton, Z. F. (2004). α-amanitin blocks translocation by human RNA polymerase II. The Journal of Biological Chemistry, 279, 27422-27427. http://dx.doi.org/10.1074/jbc.M402163200.

Griffiths, A. J. F., Miller, J. H., Suzuki, D. T., Lewontin, R. C., and Gelbart, W. M. (2000). Transcription and RNA polymerase. In An introduction to genetic analysis (7th ed.). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK22085/.

Inverted repeat. (2016, February 13). Retrieved February 13, 2016 from Wikipedia: https://en.wikipedia.org/wiki/Inverted_repeat.

Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., and Darnell, J. (2000). Bacterial transcription initiation. In Molecular cell biology (4th ed., section 10.2). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK21612/.

Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., and Darnell, J. (2000). RNA polymerase II transcription-initiation complex. In Molecular cell biology (4th ed., section 10.6). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK21610/.

Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., and Darnell, J. (2000). Transcription termination. In Molecular cell biology (4th ed., section 11.1). New York, NY: W. H. Freeman. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK21601/.

Moran, L. A. (2008, September 16). How RNA polymerase binds to DNA [Web log post]. In Sandwalk: Strolling with a skeptical biochemist. Retrieved from http://sandwalk.blogspot.com/2008/09/how-rna-polymerase-binds-to-dna.html

OpenStax College, Biology. (2016, March 23). Eukaryotic transcription. In OpenStax CNX. Retrieved from http://cnx.org/contents/GFy_h8cu@10.8:6l70P9u6@5/Eukaryotic-Transcription.

OpenStax College, Concepts of Biology. (2016, October 31). Transcription. In OpenStax CNX. Retrieved from http://cnx.org/contents/s8Hh0oOc@9.11:TkuNUJis@3/Transcription.

Polyadenylation. (2016, January 24). Retrieved February 11, 2016 from Wikipedia: https://en.wikipedia.org/wiki/Polyadenylation.

Purves, W. K., Sadava, D. E., Orians, G. H., and Heller, H.C. (2004). Transcription: DNA-directed RNA synthesis. In Life: the science of biology (7th ed., pp. 237-239). Sunderland, MA: Sinauer Associates.

Raven, P. H., Johnson, G. B., Mason, K. A., Losos, J. B., and Singer, S. R. (2014). Genes and how they work. In Biology (10th ed., AP ed., pp. 278-303). New York, NY: McGraw-Hill.

Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Transcription is the DNA-directed synthesis of RNA: A closer look. In Campbell biology (10th ed., pp. 340-342). San Francisco, CA: Pearson.

Rho factor. (2016, October 19). Retrieved November 20, 2016 from Wikipedia: https://en.wikipedia.org/wiki/Rho_factor.

Richard, P. and Manley, J. L. (2009). Transcription termination by nuclear RNA polymerases. Genes & Dev., 23, 1247-1269. http://genesdev.cshlp.org/content/23/11/1247.full.

Saunders, A., Core, L. J., and Lis, J. T. (2006). Breaking barriers to transcription elongation. Nature Reviews Molecular Cell Biology, 7, 557-567. http://dx.doi.org/10.1038/nrm1981.

Terminator (genetics). (2015, December 14). Retrieved February 13, 2016 from Wikipedia: https://en.wikipedia.org/wiki/Terminator_%28genetics%29.

Webb, S. Witte, L., Wong, K., Woreta, T., and Yoo, E. (2002, May 8). TFIIH. In RNA polymerase II in eukaryotes and prokaryotes. Retrieved from http://www.biochem.umd.edu/biochem/kahn/molmachines/newpolII/TFIIH.html.

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AlaaBaqer25
Posted 7 years ago. Direct link to AlaaBaqer25's post “What is the benefit of th...”
What is the benefit of the coding strand if it doesn't get transcribed and only the template strand gets transcribed? Please answer asap. Thank you!
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(17 votes)
Answer
- Daniel
  Posted 7 years ago. Direct link to Daniel's post “Having 2 strands is essen...”
  Having 2 strands is essential in the DNA replication process, where both strands act as a template in creating a copy of the DNA and repairing damage to the DNA. Additionally the process of transcription is directional with the coding strand acting as the template strand for genes that are being transcribed the other way.
  In the diagrams used in this article the RNA polymerase is moving from left to right with the bottom strand of DNA as the template. If the promoter orientated the RNA polymerase to go in the other direction, right to left, because it must move along the template from 3' to 5' then the top DNA strand would be the template.
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  (26 votes)
Selena Hostetler
Posted 8 years ago. Direct link to Selena Hostetler's post “Why does RNA have the bas...”
Why does RNA have the base uracil instead of thymine?
Button navigates to signup pageComment on Selena Hostetler's post “Why does RNA have the bas...”
(4 votes)
Answer
- Darmon
  Posted 8 years ago. Direct link to Darmon's post “To add to the above answe...”
  To add to the above answer, uracil is also less stable than thymine. RNA molecules are constantly being taken apart and put together in a cell, and the lower stability of uracil makes these processes smoother. In DNA, however, the stability provided by thymine is necessary to prevent mutations and errors in the cell's genetic code. :)
  Button navigates to signup page
  (35 votes)
gazar3049
Posted 4 years ago. Direct link to gazar3049's post “During DNA replication ,D...”
During DNA replication ,DNA ligase enzyme is used alongwith DNA polymerase enzyme so during transcription is RNA ligase enzyme also used along with RNA polymerase enzyme to complete the phosphodiester backbone of the mRNA between the gaps?
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(6 votes)
Answer
- Ivana - Science trainee
  Posted 4 years ago. Direct link to Ivana - Science trainee's post “*Great question*! Not du...”
  Great question!
  
  Not during normal transcription, but in case RNA has to be modified, e.g. bacteriophage, there is T4 RNA ligase (Prokaryotic enzyme).
  (s the ability of bacteriophage T4 to rescue essential tRNAs nicked by host
  nucleases, or in the more exotic RNA editing processes
  seen in kinetoplastids, in which mRNA molecules are
  cut, their coding sequence altered, and then the RNA
  pieces spliced back together).
  
  Nucleotidyl transferases share the same basic mechanism, which is the case of RNA ligase begins with a molecule of ATP is attacked by a nucleophilic lysine, adenylating the enzyme and releasing pyrophosphate.
  
  https://www.cell.com/molecular-cell/pdf/S1097-2765(04)00089-9.pdf
  
  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4234903/
  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1624903/
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  (4 votes)
Emma Hong
Posted 7 years ago. Direct link to Emma Hong's post “i heard ATP is necessary ...”
i heard ATP is necessary for transcription. Which process does it go in and where? (initiation, elongation, termination)
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(4 votes)
Answer
- nidanazar1
  Posted 7 years ago. Direct link to nidanazar1's post “ATP is need at point wher...”
  ATP is need at point where transcription facters get attached with promoter region of DNA , addition of nucleotides also need energy durring elongation and there is also need of energy when stop codon reached and mRNA deattached from DNA. There for termination reached when poly Adenine region appeared on DNA templet because less energy is required to break two hydrogen bonds rather than three hydrogen bonds of c, G. transcription process starts after a strong signal it will not starts on a weak signals because its energy consuming process.
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  (3 votes)
Hansika JS
Posted 2 years ago. Direct link to Hansika JS's post “What about termination in...”
What about termination in eukaryotes?
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(4 votes)
Answer
- Evan Ding
  Posted a year ago. Direct link to Evan Ding's post “Termination in eukaryotes...”
  Termination in eukaryotes is much more complex and varies depending on the gene and organism. But generally, as mentioned in the article, a polyadenylation signal is released, which attracts rna cleavage proteins (which also varies!) and cuts the mRNA off.
  Button navigates to signup page
  (2 votes)
nguyebre
Posted 2 years ago. Direct link to nguyebre's post “Concerning Rho-independen...”
Concerning Rho-independent termination, why does the RNA fold back onto itself after reaching the C-G rich region, I get the purpose of the stable bonds formed by C-G nucleotides, but I'm just confused about the folding.
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(2 votes)
Answer
- FrozenPhoenix45
  Posted 2 years ago. Direct link to FrozenPhoenix45's post “If you had, say, a paper ...”
  If you had, say, a paper clip, and you stretched it out so the wire was straight, and then hold it by one end and press it into a wall, what would happen? The wire would bend back in on itself because it no longer has anywhere else to go in that direction, but its momentum forces it to go somewhere, making it bend in a different direction. I believe that is what occurs when the RNA hits the terminator.
  
  I hope this helped! Comment if you have any questions; I'll answer to the best of my ability.
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  (5 votes)
mac mike
Posted 6 years ago. Direct link to mac mike's post “so there are many promote...”
so there are many promoter regions in a DNA, which means how RNA Polymerase know which promoter to start bind with. what triggers particular promoter region to start depending upon situation.
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(3 votes)
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- tyersome
  Posted 6 years ago. Direct link to tyersome's post “This is a good question, ...”
  This is a good question, but far too complex to answer here. In fact, this is an area of active research and so a complete answer is still being worked out.
  
  There are many known factors that affect whether a gene is transcribed. These include factors that alter the accessibility of chromatin (chromatin remodeling), and factors that more-or-less directly regulate transcription (e.g transcription factors).
  
  Also worth noting that there are many copies of the RNA polymerase complex present in each cell — one reference§ suggests that there could be hundreds to thousands of separate transcription reactions occurring simultaneously in a single cell!
  
  The following are a couple of other sections of KhanAcademy that provide an introduction to this fascinating area of study:
  https://www.khanacademy.org/science/biology/gene-regulation
  
  https://www.khanacademy.org/test-prep/mcat/biomolecules#gene-control
  
  §Reference:
  https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926752/
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  (2 votes)
maria murcia
Posted 7 years ago. Direct link to maria murcia's post “Hi, very nice article. Ho...”
Hi, very nice article. How may I reference it? I'm interested in eukaryotic transcription. Both links provided in 'Attribution and references' go to Prokaryotic transcription but not eukaryotic. Thank you
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(3 votes)
Answer
Hanna Rudnytska
Posted 2 years ago. Direct link to Hanna Rudnytska's post “Do promoters and terminat...”
Do promoters and terminators get copied into the new transcript? Are they are part of the new RNA transcript after transcription has ended?
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Answer
- FrozenPhoenix45
  Posted 2 years ago. Direct link to FrozenPhoenix45's post “Promoters and terminators...”
  Promoters and terminators do not get copied into the new transcript. The promoter is there to tell the RNA to "get ready" and signal the start of the transcription site. The RNA binds to it, but does not copy it. The same is true of the terminator. It stops the RNA's momentum, letting it know that it needs to stop transcribing. In Rho-dependant reactions, I do not believe the terminator could be copied by the RNA anyway. So the answer to your question is no, the promoters and terminators are not copied.
  
  I hope this helped! Comment if you have any questions; I'll answer to the best of my ability.
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Jazmine Aguilar
Posted 5 years ago. Direct link to Jazmine Aguilar's post “According to my notes fro...”
According to my notes from my biochemistry class, they say that the rho factor binds to the c-rich region in the rho dependent termination, not the independent. Therefore, in order for termination to occur, rho binds to the region which contains helicase activity and unwinds the 3' end of the transcript from the template. However, if I am reading correctly, the article says that rho binds to the C-rich protein in the rho independent termination. I am still a bit confused with what is correct.
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(2 votes)
Answer
- Ivana - Science trainee
  Posted 5 years ago. Direct link to Ivana - Science trainee's post “The article says that in ...”
  The article says that in Rho-independent termination, RNA polymerase stumbles upon rich C region which causes mRNA to fold on itself (to connect C and Gs) creating hairpin. That hairpin makes Polymerase stuck and termination of elongation.
  
  I do not see the Rho factor mentioned in the text nor on the photo.
  
  Probably those Cs and Gs confused you.
  
  :D
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  (2 votes)