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BChem Transcription
For my final
| Question | Answer |
|---|---|
| Genetic information encoding protons and structural RNAs is contained in _ genes flanked by _ sites | structural, regulatory |
| Direct the initiation and termination of transcription. | regulatory sites |
| In prokaryotes, most structural genes are found in _ | operons |
| In prokaryotes, genes that encode molecules with common functions are transcribed as ____ | single RNA/polycistronic RNA |
| Eukaryotes utilized single genes with complex _ _ and often introns (_ _). | control signals, intervening sequences |
| In eukaryotes, introns are removed from the _ _ | primary transcript |
| The sense strand of the DNA has the same sequence as ___ | mRNA |
| The mRNA is complementary to the _ strand of DNA | antisense |
| mRNA contains _ | codons |
| tRNA contains _ | anticodons |
| _ are translated into polypeptides | anticodons |
| Does RNA polymerase contain proofreading? | no |
| Mg2+ (A) promotes _ of the 3' OH of the primer base | deprotonation |
| During 2 metal ion catalysis, the O- on what phosphate is nucleophilically attacked? | alpha |
| Mg 2+ B orients the incoming _ by interacting with the β & γ phosphates. | base |
| Mg2+ B facilitates the formation of the _ _ and ultimately for the departure of _ | transition state, Ppi |
| E. coli RNAP _ is a large 450 kD complex | holoenzyme |
| The subunit stoichiometry of RNAP is σ(ββ’α 2 ω),core. What does the the σ subunit do? | recognize the promoter sequence |
| The subunit stoichiometry of RNAP is σ(ββ’α 2 ω),core. What does the the α subunit do? | recognized the promoter sequence (UP element) |
| The subunit stoichiometry of RNAP is σ(ββ’α 2 ω),core. What does the the β subunit do? | catalytic domain |
| The subunit stoichiometry of RNAP is σ(ββ’α 2 ω),core. What does the the β' subunit do? | DNA binding domain |
| By using different sigma factors, the cell can regulate different classes of _ | genes |
| Which are the regions recognized by sigma factors in bacteria? | -35,-10 |
| In E. Coli,_. _ has many different sigma factors, many involved in sporulation | B. subtilus |
| σ factors are specific for phage genes, shuts off host gene transcription | bacteria phage |
| σ factors are used for the rapid scanning of the DNA for _ | promoters |
| After transcription initiation in bacteria, these are released. | sigma factors |
| in bacteria, the holoenzyme has a _ affinity for DNA | low |
| How the holoenzyme moves along the DNA in bacterial transcription initiation | diffusion |
| Bacterial transcription initiation: the enzyme binds to the promotor region, approximately _ bp 5' to start site | 40 |
| Bacterial transcription initiation: enzyme binds to promotor sequence with _ affinity | high |
| How many faces of the DNA does the enzyme bind in bacterial transcription initiation? | 1 |
| The bacterial transcription initiation enzyme binds one face of the DNA, so the complex is _ | closed |
| Bacterial Transcription Initiation: enzyme melts DNA at _ region (_-->_) | -10,-9,2 |
| Bacterial Transcription Initiation: enzyme melts DNA to create a _ complex | open |
| Bacterial Transcription Initiation: the open complex formation: the conformational change in _ guides the strand into the _ _ _ | sigma, active site tunnel |
| Bacterial Transcription Initiation: after the strand is in the active site tunnel, the initiating nucleotides _ and _ | bind, join |
| What step of bacterial transcription initiation sees a lot of aborted transcription> | open complex formation |
| Bacterial transcription always begins with the coupling of 2 __ | NTPs |
| The first of the NTP pair in bacterial transcription is almost always a _ | purine |
| Does the bacterial transcription initiation process, where 2 NTPs bind, require a primer? | No |
| Bacterial Transcription Initiation: Promoter escape is the transition between _ and _ | initiation, elongation |
| Besides in open complex formation, where are there a lot of aborted transcripts in bacterial transcription initation? | promoter escape |
| In E. coli promoter escape, the first _ occurs and the _ subunit is released. A tight binding of the ternary complex occurs. | translocation, sigma |
| Bacterial transcription elongation: _ and _ of DNA, both thought to be passive processes (no energy input) | unwinding, re-annealing |
| During transcription elongation, the active site has a short region of _ | RNA:DNA hybrid |
| The incoming nucleotides during bacterial elongtation basepair with template in _ base pairs | WC |
| The two types of transcription terminators in bacteria | Rho-dependent, Rho-independent |
| Rho dependent terminators contain a region of _ symmetry and a string of >6_ in DNA | dyad, A |
| In E. coli transcription Rho-independent termination, _ _ _ and _’s in mRNA reduces DNA:RNA contacts and causes the polymerase to fall off. | RNA secondary structure,UUUU |
| In Rho independent termination, the incorporation of _ and/or 5 _ decreases termination | I,BrU |
| I:C_G:C | < |
| Rho dependent terminators – contain region of dyad symmetry in DNA, which causes RNA polymerase to _. It also acts as a barrier to _ | dyad, pause, nucleases |
| Rho is what? | helicase |
| Rho can unwind _:_ and _:_ double helices | DNA:RNA, RNA:RNA |
| Rho binds specific sequences in RNA, like multiple _ or _ _ | C, CA |
| Rho hydrolyzes _ to propel it along the RNA 5'-->3' until it catches the _ _ | NTP, RNA polymerase |
| How does Rho destabilize the RNA polymerase:DNA interaction? | It unwinsd the RNA-DNA hybrid |
| Rho may also bind _ and cause a conformational change that enhances __. | polymerase, termination |
| The Rho protein is __, so it has 6 identical subunits | hexameric |
| the Rho protein is an ATP-_ helicase | dependent |
| In prokaryotes, Rho-dependent termination: 3’-end of transcript contains a _-rich sequence known as _ for Rho utilization. | CA, rut |
| Eukaryotes contain _ distinct RNAP activites that are responsible for synthesizing different types of RNA | three |
| Where is RNAP I located? | Within the nucleoli |
| RNA polymerase is also known as | RNAP I |
| What does RNAP I do? | synthesizes precursors of most rRNAs |
| RNAP I sees _-specific promoter recognition | species |
| RNAP I: __-> ___ required for high level expression. Binds transcription factors. | -187,-107 |
| RNAP I: _->_ required for proper initiation | -31, +6 |
| Where is RNAP II located? | nucleoplasm |
| What does RNAP II do? | synthesizes mRNA recursors, recognizes promoters |
| What does RNAP II depend on? | transcription factors |
| Promoters contain a large number of _ _ for different factors | binding sites |
| TATA (-25) | helps determine start site |
| CCAAT (-70-->-90) | increases rate of transcription initation |
| GGGCGG | found in housekeeping genes, increases rate of initation |
| Enhancers- work at a distance in either orientation to increase __. | RNA II |
| Where is RNAP III located? | Within the nucleoplasm |
| What does RNAP III do? | synthesizes precursors of 5S rRNAs, tRNAs, and other small nuclear and cytosolic RNAs |
| Where are organelle polymerases found? | chloroplast, mitochondria |
| Organelle polymerases are similar to what? | RNA polymerases |
| Eukaryotic polymerases are large and complex, with at least _ subunits | 10 |
| Eukaryotic polymerases have a large number of _ factors, _ factors and _ factors. | initiation, elongation, termination |
| Eukaryotic Transcription Initiation: what two things affect the formation/transition of both the initiation and elongation complexes? | chromatin structure and DNA seuqence |
| Eukaryotic Transcription Initiation: these proteins remodel the chromatin by moving nucleosomes, as well as control transcription activity | SWI, SNF, NURF |
| How do SWI, SNF, and NURF control transcriptional activity? | Pre-initiation complex assembly, promoter escape and early elongation stages. |
| TFIIB | Binds TBP and recruits Pol II and TFIIF |
| TFIIF-Pol II | Adapter between Pol II and TFIIB |
| TFIIE | Recruits TFIIH |
| TFIIH | helicase, unwinds DNA at promoter, PO4 Pol II CTD |
| TBP | specifically regonzines the TATA box |
| Pol II | catalyzes RNA synthesis |
| What's the inchworm model of elongation presume> | Two DNA binding sites can move independent of one another. |
| RNA is held to polymerase by the two __ binding sites in the inchworm model | RNA |
| E Elongation: the catalytic site is located at upstream edge of __ | DNA binding site I |
| E Elongation: the catalytic site adds _ nucleotides as it moves along DNA site I | about 10 |
| While the catalytic site moves along DNA site I, DNA site I is __ and DNA site II is __ with the catalytic site | fixed, moving |
| E Elongation: at the end of nucleotide addition, RNA and DNA sites _ become fixed and DNA binding site _ translocates 10 bases to start again. | II, I |
| In E. Elongation, Crystal structure suggests that _ portion of enzyme undergoes a conformational change after each addition step to move the enzyme down the DNA | bridge |
| Why are inhibitors useful in elongation? | chemotherapy and mechanistic studies |
| Name 4 elongation inhibitors. | intercalating agents, amatoxins, rifamycis, cordycepin |
| Inercalating agents contain __ aromatic rings that fit between base pairs, blocking what? | planer, DNA and RNA synthesis |
| Give examples of intercalating agents. | Daunomycin, Adriamycin, Actinomycin D, EtBr, Proflavin |
| Amatoxins are one of the poisons in _ | mushrooms |
| a-amanitin is a bicyclic octpeptide that binds 1:1 with _ and inhibits elongation | Pol II, Pol III |
| Rifamycins only inhibit what kind of polymerases? | prokaryotic. |
| Rifamycins They bind pol and block elongation from _ to _ nuc. | second, third |
| What happens if rifamycins are added later? | Rifamycins do not block initiation or later elongation |
| What does late addition rifamycin indicate? | confomrational difference |
| What does cordycepin, a 3'deoxyadenosine, do? | When incorporated into growing chain,causes termination. |
| Which inhibitor indicated elongation is 5' to 3"? | cordycepin |
| During transcription, a DNA sequence is read by an RNA polymerase, producting an RNA strand that is both __ and __ | complementary, antiparallel |
Created by:
ScarlettRose