An in-depth looks at how transcription works. Initiation (promoters), elongation, and termination.
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! • (17 votes) 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. (26 votes) Why does RNA have the base uracil instead of thymine? • (4 votes) 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. :) (34 votes) 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? • (6 votes) Great question! Not during normal transcription, but in case RNA has to be modified, e.g. bacteriophage, there is T4 RNA ligase (Prokaryotic enzyme). 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/ (4 votes) i heard ATP is necessary for transcription. Which process does it go in and where? (initiation, elongation, termination) • (4 votes) 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. (3 votes) What about termination in eukaryotes? • (4 votes) 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. (2 votes) 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. • (3 votes) 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/test-prep/mcat/biomolecules#gene-control §Reference: (2 votes) 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 • (3 votes) Do promoters and terminators get copied into the new transcript? Are they are part of the new RNA transcript after transcription has ended? • (2 votes) 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. (3 votes) 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. • (2 votes) 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. (3 votes) 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. • (2 votes) 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 (2 votes)Want to join the conversation?
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.
(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).
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1624903/
https://www.khanacademy.org/science/biology/gene-regulation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2926752/
Understanding transcription requires diving into molecular processes crucial for genetic information transfer. I can break down each component.
Promoters: These are DNA sequences signaling where transcription should commence. They're vital in regulating gene expression and determining the starting point for RNA synthesis.
Elongation: During this phase, RNA polymerase moves along the DNA template, creating an RNA strand complementary to the DNA strand. The coding strand acts as the template for gene transcription, guiding RNA polymerase in the direction necessary for RNA synthesis.
Termination: There are two types: Rho-dependent and Rho-independent. Rho-dependent termination involves a termination factor binding to a specific region, prompting RNA release. Rho-independent termination happens when the RNA strand folds into a hairpin structure, halting RNA polymerase and leading to termination.
Coding Strand vs. Template Strand: Both strands play roles in different processes. The coding strand (non-template) doesn't directly participate in transcription but carries the same sequence as the RNA transcript, barring T's in DNA and U's in RNA. The template strand guides RNA polymerase to generate the complementary RNA sequence.
Thymine vs. Uracil in DNA and RNA: RNA uses uracil instead of thymine. Uracil's lower stability compared to thymine aids in RNA's constant disassembly and reassembly within cells, facilitating smoother processes. Thymine's stability in DNA helps prevent mutations and errors in genetic coding.
Energy Requirements and Enzymes in Transcription: ATP is essential in transcription, primarily during initiation, elongation (nucleotide addition), and termination steps. Enzymes like RNA polymerase catalyze RNA synthesis without the involvement of RNA ligase in normal transcription processes.
Transcription Factors and Promoter Selection: Transcription factors and chromatin accessibility regulate gene transcription. Multiple factors, including chromatin remodeling and specific transcription factors, dictate which genes are transcribed and the promoter regions chosen for initiation.
Promoter and Terminator Inclusion in RNA Transcript: Promoters and terminators are not copied into the RNA transcript. Promoters signal the starting point, while terminators indicate where transcription should cease without becoming part of the final RNA product.
Rho-Dependent and Rho-Independent Termination: Rho-dependent termination involves a factor binding to a specific region to prompt RNA release, while in Rho-independent termination, RNA folding creates a hairpin structure that halts RNA polymerase.
Rho Factor and RNA Polymerase Interaction: Confusion might arise regarding the interaction between the Rho factor and termination. Rho-dependent termination involves the Rho factor binding to a specific region, while Rho-independent termination occurs due to RNA folding creating a hairpin structure.
Understanding these concepts paints a comprehensive picture of transcription, an intricate process crucial for genetic expression and cellular function.
