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BCHM 4360 ACTUAL EXAM 3 2025 VERIFIED RATIONALES WITH COMPLETE
SOLUTIONS GRADED A
Splicing machinery Elongation leads to more phosphorylation of CTD, which recruits Cleavage and polyadenylation complex Elongation also leads to recruitment of the Nucleus Transcription and processing of eukaryotic mRNA occurs in the Cytoplasm Translation occurs in the Exported Mature mRNAs must be ______________ from the nucleus Polyadenylation The protein factors needed for transport are loaded onto the mRNA during transcription, but __________________ is needed before the RNA-protein complex can be released from the transcription complex
Localization elements Some mRNAs are located in specific regions of the cytoplasm, this requires ______________________, usually found at the 3' end -- they also regulate translation snoRNAs and certain miRNAs Most introns do not contain genes and are excised and degraded. Exceptions are Transesterification Some introns are removed by proteins, some by RNPs, and some excise themselves. All mechanisms use ______________________ reactions Eukaryotes Introns are far more prevalent in _____________________ Exon shuffling Introns allow for ____________________, where exons are exchanged and reordered via recombination, allowing evolution of different genes Same Differential removal of introns gives different transcripts from the _______________ gene
Group I introns This group of introns are found in bacteria, viruses, microeukaryotes, and plants 120 - 450 Group I introns are ______________ nucleotides long Group I introns Many but not all of this group of introns can excise themselves from the primary transcript Group I introns In this group of introns, splice sites are determined by the 3D structure of the intron and by recognition of a conserved G-U wobble pair Group I introns (which group of introns) In the first transesterification, a free guanosine is the attacking species that detaches the 5' end of the intron from exon 1 In the second reaction, the released end of exon 1 attacks the intron-exon 2 junction, joining the two exons together
Group II introns This group of introns are in bacteria and organellar genes of plants and fungi Group II introns This group of introns are 400-1000 nucleotides long Group II introns (which group of introns) 2' OH of a specific A within the intron attacks the exon 1-intron junction Once released, the intron forms a branched lariat intermediate Group II introns In this group of introns, the splice sites are determined by the 3D structure of the intron Group II introns This group of introns can also act as mobile genetic elements by reverse splicing, and they often have open reading frames within the introns that assist splicing
Pre-RNAs need to be modified to make the mature, functional RNA This process is called Regulation One of three benefits of RNA processing Diversity One of three benefits of RNA processing Quality control One of three benefits of RNA processing Ribonucleoproteins (RNPs) Many of the RNA processing complexes contain both protein and RNA, these are called Ribozymes The RNA in ribonucleoproteins (RNPs) can be structural, but they can also have catalytic activities and are therefore called
Structural The RNA in ribonucleoproteins (RNPs) can be ___________________, but they can also have catalytic activities and are therefore called ribozymes Guide RNAs Some ribonucleoproteins (RNPs) contain __________________ which base pair with pre- RNAs and guide the RNP to the correct place for processing tRNA and rRNA These type of RNA transcripts are made as long precursors that must be processed E. coli precursor Encodes three rRNAs and several tRNAs S. cerevisiae precursor Encodes three rRNAs Exonucleases Successively remove nucleotides from the end of a transcript 3' to 5'
RNase III During excision of bacterial rRNAs, this ribonuclease bends stem structures in the pre- RNAs and cleaves the dsRNAs RNase P 5' trimming of tRNAs is done by this ribonuclease RNase P This ribonuclease has an RNA component and proteins Bacterial In RNase P, the _______________ RNA component alone can cut RNA, and the protein part enhances the activity and may determine substrate range Eukaryotic, archaeal, and mitochondrial In RNase P, the ____________________ RNA component cannot cut RNA alone, but is essential for function Protein factors Introns are present in some tRNAs. tRNA splicing is catalyzed by
Self splicing Introns are present in some rRNAs. Some rRNA introns can catalyze their own removal and are therefore ________________ Precursor RNAs therefore act as ribozymes themselves CCA The 3' ends of tRNAs have a conserved _____________ sequence CCA sequence The tRNA attachment site for the amino acid Encoded The CCA at the 3' end of tRNAs is sometimes ________________ by the tRNA gene CCA adding enzyme The CCA at the 3' end of tRNA is most often added later by a Nucleotide binding pocket
The enzymes that catalyze ribose methylation and the uridine to pseudouridine transition are similar in all organisms, but the ____________________________ are different Small nucleolar RNAs (snoRNAs) Eukaryotes and archaea use _______________ to guide enzymes to the correct site snoRNP Small nucleolar RNAs (snoRNAs) associate with a complex of proteins to make an RNP called Small nucleolar RNAs (snoRNAs) Found in the nucleolus 60 - 300 nucleotides long Made from the introns of precursor mRNAs Small nucleolar RNAs (snoRNAs) Base pairs with specific regions of target RNAs and directs enzymes to those positions for ribose methylation/pseudouridylation Box C/D snoRNAs
snoRNAs that direct ribose methylation H/ACA snoRNAs snoRNAs that direct pseudouridylation 7 - methylguanine nucleotide The 5' ends are capped with a 5'-5' triphosphate linkage The 5' ends are capped with a 7-methylguanine nucleotide via a N Guanine is then methylated at N7 during 5' capping Elongation and termination 5' cap is needed for efficient mRNA processing 5' cap is needed for efficient
Different In yeast, the three steps of 5' capping are done by _______________ enzymes Single In C. elegans and mammals, the first two steps of 5' capping are done by a ________________ enzyme Initial cleavage Polyadenylation at the 3' end of eukaryotic mRNAs starts with an CA Initial cleavage during polyadenylation usually occurs after a __________ that lies between an AAUAAA hexamer and U or GU rich region 200 After the initial cleavage during polyadenylation, around this many adenosines are added by poly(A) polymerase Larger A _______________ protein complex is required for polyadenylation than for 5' capping, probably because it is more complex to recognize the different polyadenylation sites in different mRNAs
Multiple ________________ polyadenylation sites are found in some mRNAs, such as cyclin D mRNA, and these can participate in regulation Distal Polyadenylation at the ______________ site retains multiple regulatory sequences Proximal Polyadenylation at the __________________ site eliminates the regulatory sequences 5' capping This is needed to allow RNA pol II to continue transcription 3' polyadenylation This is needed for efficient transcription termination Rpb The C-terminal domain (CTD) of the largest subunit of RNA pol II, _____________, is responsible for mediating mRNA processing
5, U1, U2, U4, U5, U
The spliceosome has _________ snRNPs, which are snRNA The spliceosome has 5 snRNPs (U1, U2, U4, U5, U6). Each has an ____________ of about 100 - 300 nucleotides, plus proteins Recognition The snRNAs of the snRNPS of the spliceosome form base pairs with the pre-mRNA and work as the _________________ part of the snRNP U Splicing by spliceosome in eukaryotes Step 1 - The 5' splice site is recognized by ____________ and other sequences are bound by non-snRNPs Branch point binding protein (BBP) Splicing by spliceosome in eukaryotes
Steps 2 and 3 - The rest of the splicing apparatus binds, sometimes displacing other factors, including the ___________________ Lariat Splicing by spliceosomes in eukaryotes Step 4 - The pre-mRNA rearranges. The first transesterification occurs and the _____________ forms Transesterification Splicing by spliceosomes in eukaryotes Step 5 - Other rearrangements then bring the two exons for the second ___________________ Exon junction complex (EJC) Left at splice junctions after splicing Marks the transcript as processed and interacts with export and translation proteins Cis splicing Where exons in the same molecule are joined together
