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RNA Metabolism
Biochem Ch. 29
| Question | Answer |
|---|---|
| What process does RNA Polymerase catalyze? | RNA Polymerases catalyze RNA Synthesis, aka, Transcription. |
| Which is there more of within a cell - DNA or RNA? | There is more RNA within a cell than there is DNA. |
| Which is metabolized more often - DNA or RNA? | RNA is metabolized more often the DNA. |
| RNA Polymerase of E. Coli (a Prokaryote) was discovered first. How many sub-units does it have? | Prokaryotic RNA Polymerase has 4 types of sub-units. (2) Alpha, (1) Beta, (1) Beta prime, and (1) Sigma sub-unit. |
| Which sub-units of Prokaryotic RNA Polymerase has a Eukaryotic Homolog? | The Sigma sub unit of Prokaryotic RNA Polymerase is the only sub-unit that does not have a Eukaryotic Homolog. |
| What is Transcription? | Transcription is the process where RNA is made using DNA as a template. |
| What is Footprinting? | Footprinting is a protection assay. It uses a DNA-ase to find, or identify cis-elements. It's a technique for determining where on a DNA molecule a protein is bound. |
| To what end of the newly-formed strand does RNA Polymerase add nucleotides to? | RNA Polymerase adds nucleotides to the 3'-end of a growing chain. |
| In what direction does RNA Polymerase work? | RNA Polymerase polymerizes in the 5'-3' direction. The 3 phosphates of the incoming Ribonucleoside-triphosphate are on the 5' end of the RNA. |
| What bonds are broken and made by RNA Polymerase? | There are 3 phosphates on the 5'-end of the incoming RiboNucleotide-TriPhosphates. RNA POL breaks the bond between the alpha & beta phosphates of the RNA's 5' end, and then forms a new bond between the Template's 3'OH, and the nucleotide's alpha phosphate |
| What are the substrates of RNA Pol? | RNA Polymerase requires RNTPs, (2) ATP/ATP equivalents, and a DNA template strand. |
| What are the products of RNA Pol? | Inorganic PyroPhosphate (IPP), and, the new RNA strand that is now a nucleotide-length longer. |
| What direction are newly formed RNA and DNA strands made? | RNA chains, like DNA chains grow in the 5'-3' direction. |
| Some Antibiotics can target what process? | Some Antibiotics can target TRANSLATION. Antibiotics are frequently designed to target various aspects of translation. |
| E. Coli can switch from making one class of genes to make another class of genes, due to changes of circumstances. What are they? | Switching of classes of genes in E.Coli can happen as a result of changing which Sigma-factor is being synthesized. |
| What types of RNA do cells make? | mRNA, tRNA, rRNA. |
| What is the role of mRNA? | It carries message to be translated into protein. |
| What is the role of tRNA? | It carries amino acids to ribosomes for incorporation into protein. |
| What is the role of rRNA? | components of ribosomes. |
| How do Prokaryotic Promoters control the rates at which Transcription Initiation is stimulated? | Prokaryote Promoters control such events by variation in the -10 Pribnow & -35 Box conserved sequences. The closer a given promoter's sequence matches the consensus sequence of the -10 sequence, the more active the promoter is at initiating transcription. |
| Where does Transcription Initiation occur? | Transcription Initiation happens at Cis-elements in the DNA, called Promoters. |
| In transcription, we are polymerizing a nucleic acid in what direction? | We are polymerizing a nucleic acid in the 5'-3' direction. |
| In transcription, we are reading the template, or Antisense Strand in what direction? | In transcription, the Template or Antisense strand is read in the 3'-5' direction. |
| The "Transcription Start Site" is usually an A-base located at what position? | "Transcription Start Site" is usually an A-base located at +1 position, which is the 3'-end of the Template or Antisense Strand. |
| In the transcription Bubble, RNA is partly base paired with what? | The RNA is partly base paired to the template strand, with the 5' end of the RNA "hanging" off. |
| Ahead of the Transcription Bubble, what kind of supercoiling happens? | Ahead of the bubble, positive supercoils are created. This superhelical tension is relieved by DNA Gyrase. |
| Behind the Transcription Bubble, what kind of supercoiling happens? | Behind the bubble, negative supercoiling occurs, and this is relieved by a topoisomerase |
| During Prokaryotic Transcription initiation phase, what is released from RNA polymerase. | sigma factor is released from RNA polymerase |
| The factor involved in factor dependent transcription termination in E. coli is called what? | rho. |
| What does Rho bind to? | It binds to the 5' end of an RNA being made and (using ATP energy) "climbs" the RNA until it reaches the RNA polymerase. |
| Do Promoters include the Transcription Start Site? | Yes |
| U2 and U6 are types of what unit/complexes? | U2 and U6 are types snRNP's, Small Nuclear Ribonucleoprotein Particles (Only in Eukaryotes). |
| What type of Eukaryotic RNA Pol makes rRNA? | Eukaryotic RNA Pol I |
| What type of Eukaryotic RNA Pol makes tRNA? | Eukaryotic RNA Pol III |
| What type of Eukaryotic RNA Pol makes mRNA? | Eukaryotic RNA Pol II |
| What type of Eukaryotic RNA Pol makes the majority of RNA by MASS? | Eukaryotic RNA Pol I |
| What type of Eukaryotic RNA Pol makes the majority of RNA by number only, NOT mass? | Eukaryotic RNA Pol II |
| What Subunit of Eukaryotic RNA Pol II is its only well studied specific subunit? | Subunit 9 is specific to RNA Pol II. |
| Which is more accurate? Analog or Digital? | Analog is more accurate. |
| -35 Box is a cis-element in what type of Promoters? (Eukaryote or Prokaryote) | -35 Box is a cis-element ONLY in Prokaryotic Promoters. |
| -10 Box, or Pribnow is a cis-element in what type of Promoters? (Eukaryote or Prokaryote) | -10 Box, or Pribnow is a cis-element in ONLY Prokaryote Promoters. |
| Of the two conserved sequences of Prokaryote Promoters, the -10 and -35 Boxes, which one makes contact with the RNA Polymerase? | Both -10 and -35 Boxes in Prokaryotic Promoters make contact with the RNA Polymerase. |
| The RNA Pol Sigma Subunit is responsible for what? | The Prokaryotic RNA Pol Sigma Subunit is responsible for finding the -10 and -35 Box sequences in the promoters. The sigma sub-unit is responsible for promoter recognition. |
| In transcription, the DNA strand that is NOT copied, and NOT used as a template for RNA, is called what? | Coding Strand. +. The Sense Strand, because it has the same sequence as the new RNA strand (but with T, not U nucleotides). |
| In what direction does the Coding Strand, or Sense Strand run? | The Coding Strand, or Sense Strand runs 5'-3'. |
| What is the TATA-Box, or Hogness Box? | The TATA or Hogness Box is a cis-element of Eukaryotic Promoters. It's located at -25, and is DOWNstream of the Transcription Start Site. |
| Are Enhancers part of Eukaryotic Promoters? | Enhancers can be a part of Eukaryotic Promoters. |
| Are Enhancers part of Eukaryotic Basal Promoters? | No! Enhancers are NOT part of Eukaryotic Basal Promoters, since they're not common to all promoters. |
| What are the parts of the Basal Promoters of Eukaryote RNA Pol II? | Initiator which is located between -3 and +5 and includes the Transcription Start Site. The TATA or Hogness Box, located at -25 and is DOWNstream of the transcription start site. |
| TFII is what? | TFII is a transcription Factor, specific for RNA POL II transcription. It is part of the RNA-POL II transcription Basal Machinery, but is NOT a cis-element. It's a Trans-element. |
| How long (bp) is the Transcription Bubble? | 17 bp long. |
| Does the DNA template does get separated from RNA? | Yes. The DNA template does get separated from RNA. This is done by RNA Polymerase. |
| Elongation involves what? | Elongation involves the Active Site, the 5'-3' Polymerization Reaction (of which IPP is a product). |
| How does Transcription Elongation end? | Transcription Elongation ends with the new RNA-strand going out of the Transcription bubble. |
| what does snRNP stand for? | Small nuclear ribonucleoproteins |
| What is the most well-studied type of RNA polymerasese? | Yeast RNA polymerase II |
| What is a Ribosome made of? | A small subunit. Several rRNA molecules. Many accessory proteins. |
| What is responsible for the fact that there are so few introns in prokaryotic genes? | The coupling of transcription and translation |
| How many different classes of aminoacyl tRNA synthetases are there? | There are 2 classes |
| All tRNA’s have how many large hairpin loops? | All have 3. Only Some have 4. |
| The term “polycistronic” means | Several protein coding regions transcribed in the same RNA |
| Rho Dependent Transcription Termination occurs in what organisms? | Rho Dependent Transcription Termination occurs in PROKARYOTES only. |
| Transcription continues with what and ends with what? | continues with elongation and ends with termination. |
| What is the precursor or mRNA in Eukaryotes - equivalent to pre-mRNA? | hnRNA. Hetero-nuclear RNA. |
| name 3 Trans-acting factors of transcription | TBP, TFII's, Sigma Subunit |
| name 3 Trans-acting factors of Translation | Small Ribosomal Sub-unit, EF-G, EF-Tu |
| Parts of a Bacterial Operon. | A Polycistronic gene, A promoter, an operator sequence, Open Reading Frame. |
| What is CAP? | Catabolite Activating Protein. |
| Rho protein is what type of protein? | An ATP-ase. |
| When a TATA-Box IS present in a Eukaryotic promoter, what is it usually paired with? | Inr, or initiator element. |
| What snRNAs make the active center of spliceosomes? | U2 and U6 snRNAs. |
| Aminoacyl tRNA Synthetases have how many active sites? | 2 active sites. |
| What are snoRNPs? | Small NucleOLAR Ribonucleao-proteins, each of which consist of one snoRNA, and several proteins. |
Created by:
abenvie
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