Processing
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| Ribosomal RNAs occur here with tRNAs | operons
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| The secondary structure of the tRNAs and rRNAs is recognized by RNA’ses and used for? | processing
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| 1)Primary processing occurs during transcription by | RNAse III, E, F and P (ribozyme).
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| 2) rRNAs associate with | ribosomal proteins
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| 3)RNAse D M5, 16 and 23 carry out | 5’ and 3’ mature end processing.
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| 4) Methylation, which protects the rRNA from RNAses | O2Me ribose,
N6N6-dimethyl adenine.
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| Prokaryotic mRNA processing | little to none
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| Where does translation occur for prokaryotes? | nascent transcripts
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| Eukaryotic mRNA processing involves | capping, splicing, polyadenylation
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| Capping determines the site of | translation initiation
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| 7-methylG added co-transcriptionally via | 5',5'-triphosphate linkage
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| Cap can be differentially methylated where? | 2'-OH positions of first two nucleotides
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| cap-0 | no 2’-O-methyl, predominant in unicellular
organisms
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| cap-1 | first nt, predominant in multicellular organisms
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| The CAP is involved in what? | Loading of ribosome onto mRNA during translation
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| Capping: 1: The 5' terminal triphosphate of the RNA is first removed by | RNA triphosphate
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| Capping: 2: GTP is added by | guanyltransferase
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| Capping:3: the 7 position of guanosine is | methylated
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| Capping:4: mRNA is methylated by | 2'-O-methyltransferase
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| In mammalian cells, primary transcripts have heterogeneous | 3' ends
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| All mRNAs have poly-A tails except | histone mRNA
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| Poly-Adenylation requires the presence of | AAUAAA element
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| The AAUAAA element is located | 10-35 nt upstream of site of poly-A tail
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| Poly-Adenylation also requires the presence of a U or | GU rich sequence about 50 nt downstream the cleavage site
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| C & PA requires a dynamic assembly of multiprotein complexes: | CPSF, CStF, CFI, CFII
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| Poly-A synthesis is catalyzed by a template independent polymerase known as | PAP
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| Why doesn't PAP need a template? | Telomere has a defined sequence
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| 3’ Cleavage and Polyadenylation: 1: CFI and CFII cleave RNA | 10-30 nuc 3' to signal
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| 2) PolyA polymerase adds poly A tail using | ATP
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| When does the CPSF disengage from recognition site? | Tail is 10-15 nucleotides long
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| 3) The length of the tail is controlled by | PABII
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| Multiple copies of PABII bind to the Poly A tail to | increase processivity
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| 4) Poly(A) binding protein (PAB) binds the tails and organizes them into | ribonucleoprotein particles.
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| Besides organizing tails/particles, what does PAB do? | involved in regulating translation initiation, protect mRNA
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| Unlike most prokaryotic RNA transcripts, many eukaryotic transcripts | contain introns
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| Class of intron is based on its | sequence properties
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| mRNA splicing is coupled with | transcription
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| mRNA splicing occurs sequentially in what direction? | 5' to 3'
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| The transesterification reactions require | no net input of energy
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| The transesterification reactions are catalyzed by | transphosphorylation reactions
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| However the splicing process does require net energy input for | conformational changes in the RNA and the spliceosome.
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| Spliceosome is a large complex (?) with more than 50 proteins | 50-60S
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| targets include nuclear pre-mRNA transcripts that | can not self splice
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| introns spliced by same lariat mechanism found for | GII introns
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| Eukaryotic nuclei contain numerous copies of small RNAs (60 - 300 nt long) known as | snRNA
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| there are five high abundant snRNAs involved in the splicing reaction: | U1, U2, U4,
U5, and U6
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| What are RNAs complementary to? | Consensus sequences in the intron
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| Spliceosome: 1) U1 SnRNA binds the | 5’ consensus sequence.
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| 2) U2 SnRNA binds lariat sequence after the lariat is bound by | the branch
point binding protein (BBP)
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| The U2AF protein helps BBP select | the intron
branch point.
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| 3) U5 SnRNAbinds to the | 3' splice junction
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| 4) A complex between U4 and U6 helps | bring everything together
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| 5)A series of rearrangements in the spliceosome generate the correct environment for | different transesterification reactions.
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| 6) Once together, U1 and U4 are destabilized and | spliceosome is reactivated
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