Term
| depiction of RNA polymerase |
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Definition
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Term
| the role of Mg2+ in RNA polymerase |
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Definition
| part of the active site at the center of the structure |
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Term
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Definition
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Term
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Definition
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Term
| the 2 substrates required by RNA polymerase |
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Definition
-DNA template strand
-nucleoside triphosphates |
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Term
| the ribonucleoside triphosphates that are usen to synthesize RNA |
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Definition
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Term
| 2 divalent metal cations that can work in RNA polymerase |
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Definition
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Term
| depiction of complementarity between mRNA and DNA |
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Definition
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Term
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Definition
| (RNA)n residues + ribonucleoside triphosphate <--> (RNA)n+1 residues + PPi |
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Term
| difference between RNA polymerase and DNA polymerase |
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Definition
| RNA polymerase doesn't require a primer |
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Term
| depiction of the RNA strand-elongation rxn |
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Definition
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Term
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Definition
| the segments of DNA that encode the various species of RNA |
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Term
| 3 types of RNA in all cells |
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Definition
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Term
| composition of the RNA polymerase holoenzyme |
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Definition
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Term
| role of the σ subunit in the RNA polymerase holoenzyme |
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Definition
-helps to find a site where transcription begins
-participates in the initiation of RNA synthesis
-it then dissociates from the rest of the enzyme |
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Term
| composition of the RNA polymerase core enzyme |
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Definition
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Term
| table of the subunits of E. coli RNA polymerase |
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Definition
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Term
| the 3 stages of RNA synthesis |
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Definition
1: initiation
2: elongation
3: termination |
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Term
| how RNA polymerase knows where to begin transcription |
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Definition
| promoters direct it to the proper site |
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Term
| where the promoters are in DNA |
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Definition
| about 10 and 35 nucleotides upstream of the start site |
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Term
| depiction of bacterial promoter sequences |
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Definition
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Term
| depiction of consensus (average) sequences deduced from the analysis of many promoters |
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Definition
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Term
| how strength of promoter affects transcription |
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Definition
| genes with stronger promoters get transcribed more frequently |
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Term
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Definition
| regulatory proteins that bind to specific sequences near promoter sites and interact with RNA polymerase |
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Term
| how the upstream element (UP element) increases efficiency of transcription |
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Definition
| by binding to the α subunit of RNA polymerase, creating an additional binding site for the polymerase |
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Term
| the role of the σ subunit in RNA polymerase |
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Definition
| helps to recognize promoter sites |
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Term
| how the σ subunit helps RNA polymerase recognize promoter sites |
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Definition
| 1: decreases affinity of RNA polymerase for general regions of DNA by a factor of 104, allowing t to slide rapidly in search of the promoter
2: enables RNA polymerase to recognize promoter sites |
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Term
| depiction of the RNA polymerase holoenzyme complex |
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Definition
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Term
| depiction of how sigma factors act catalytically |
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Definition
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Term
| depiction of DNA unwinding |
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Definition
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Term
| depiction of RNA strand growth |
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Definition
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Term
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Definition
region containing RNA polymerase, DNA, and nascent RNA
contains "bubble" of about 17 separated base pairs |
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Term
| depiction of transcription bubble |
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Definition
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Term
| depiction of RNA-DNA hybrid separation |
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Definition
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Term
| why the higher error rate of RNA polymerase can be tolerated |
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Definition
| because mistakes in RNA are not transmitted to progeny |
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Term
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Definition
| RNA polymerase can backtrack and remove the incorrect nucleotide using its inherent nuclease activity |
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Term
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Definition
termination of DNA transcription onto RNA within or just after a GC rich stem-and-loop structure followed by 4 U residues
terminates within or just after the termination signal |
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Term
| depiction of termination signal |
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Definition
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Term
| how the combination hairpin-oligo(U) strucvture terminates transcription |
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Definition
1: RNA polymerase appears to pause immediately after synthesising sequence that folds into a hairpin
2: RNA-DNA hybrid helix in the oligo(U) tail is unstable because rU-dA base pairs are the weakest of the Watson-Crick base pairs, thus allowing the pause caused by the hairpin to dissociate from the DNA template and the enzyme |
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Term
| protein-dependent termination |
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Definition
| termination that requires the participation of with ATPase activity caller the rho (p) protein |
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Term
| how the rho (p) protein terminates RNA transcription |
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Definition
1: hexameric p gets brought into action by sequences rich in C and poor in G
2: p then races down the strand searching for the RNA polymerase
3: p collides with RNA polymerase at the transcription bubble, breaking the RNA-DNA hybrid helix, unwinding the hybrid helix and stopping transcription |
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Term
| common feature of protein-independent and protein-dependent termination |
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Definition
| the functioning signals lie in the RNA rather than the DNA |
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Term
| depiction of the mechanism for the termination of transcription by p protein |
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Definition
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Term
| tRNA and rRNA are generated by... |
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Definition
| cleavage and other modifications of the transcription product |
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Term
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Definition
| noncoding regions of RNA product |
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Term
| depiction of primary transcript of RNA |
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Definition
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Term
| S value vs. how fast RNA molecules move in a centrifugal field |
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Definition
| the larger the S value, the larger the molecule moves |
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Term
| some ways rRNA's and tRNA's are processed |
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Definition
-excision from precursor
-addition of nucleotides to the termini of some strands (common for tRNA)
-modification of bases and ribose units |
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Term
| type of RNA processing common for tRNA |
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Definition
| addition of nucleotides to termini of molecules |
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Term
| how bases and ribose units are modified in mRNA and tRNA |
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Definition
-some bases being methylated (bacteria)
-unusual bases formed in all tRNA molecules by the enzymatic modification of a standard ribonucleotide in a tRNA precursor |
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Term
| depiction of base pair modifications in RNA |
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Definition
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Term
| depiction of antibiotic action |
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Definition
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Term
| an essential enzyme in the metabolism of lactose |
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Definition
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Term
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Definition
| hydrolyzes lactose into galactose and glucose |
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Term
| depiction of β-galactosidase induction |
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Definition
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Term
| the 2 other proteins that are synthesized when β-galactosidase is synthesized |
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Definition
-galactoside permease
-thiogalactoside transacetylase |
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Term
| function of galactoside permease |
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Definition
| it is required for the transport of lactose across the bacterial cell membrane |
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Term
| function of thiogalactoside transacetylase |
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Definition
| not essential for lactose metabolism, but may play a role in the detoxification of compounds that also may be transported by the permease |
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Term
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Definition
| coordinated unit of genes that cnahge expression in response to environmental changes |
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Term
| the DNA components of the regulatory system of the lac operon |
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Definition
-regulator gene
-operator site
-set of structural genes |
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Term
| depiction of the general structure of an operon |
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Definition
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Term
| depiction of the lac operon |
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Definition
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Term
which part of the lac operon is i?
[image] |
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Definition
| the gene encoding the repressor |
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Term
which part of the lac operon is o?
[image] |
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Definition
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Term
which part of the lac operon is z?
[image] |
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Definition
| structural gene for β-galactosidase |
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Term
which part of the lac operon is y?
[image] |
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Definition
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Term
which part of the lac operon is a?
[image] |
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Definition
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Term
which part of the lac operon is p?
[image] |
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Definition
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Term
| function of the promoter site in the lac operon |
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Definition
| directs the RNA polymerase to the correct transcription-initiation site |
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Term
| function of the z, y, and a proteins |
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Definition
| they are transcribed to yield a single mRNA molecule that codes for all 3 proteins |
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Term
| polygenic or polycistronic transcript |
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Definition
| mRNA molecule encoding more than 1 protein |
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Term
| how does the lac repressor inhibit the expression of the lac operon? |
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Definition
| in the absence of lactose, the repressor binds very tightly to the operator to block the bound RNA polymerase from using the DNA as a template |
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Term
| how the repressor is removed from the lac operon |
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Definition
| inducer binds to repressor, causing a structural change that greatly reduces the affinity of the repressor for the operator DNA |
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Term
| depiction of the induction of the lac operon |
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Definition
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Term
| a type of lac operon inducer |
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Definition
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Term
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Definition
| combination of galactose and glucose with an α-1,6 rather than an α-1,4 linkage |
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Term
| what generates allolactose? |
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Definition
| it's a side product of the few molecules of β-galactosidase that are always present before induction |
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Term
| structure of 1,6-allolactose |
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Definition
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Term
| one DNA-sequence specific protein that stimulates the transcription of the lac operon when glucose is in short supply |
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Definition
| catabolite activator protein (CAP), aka cyclic AMP (cAMP) response protein (CRP) |
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Term
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Definition
| in this case, it's glucose inhibiting the expression of the lac operon |
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Term
| cellular glucose concentration vs. concentration of cAMP |
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Definition
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Term
| depiction of the binding site forcatabolite activator protein (CAP) |
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Definition
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Term
| how the level of cAMP is controlled in bacteria |
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Definition
-enzyme IIA (EIIA) is phosphorylated at the expense of the glycolytic intermediate phosphoenolpyruvate
-phosphorylated EIIA then transfers phosphate to glucose, generating G6P
-if glucose is absent, phosphorylated EIIA activates adenylate cyclase, leading to an increase in cAMP and enhanced transcription of the lac operon |
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Term
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Definition
| mRNA molecules that form secondary structures capable of binding small molecules, thus preventing further transcription of mRNA |
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