Cell Biology Quiz 2 Review Chapter 7 Modifications to the mRNA o 50 of the time the second ribonucleotide has CH3 attached to the 2 OH Confers more stability to the RNA Affects both stability and further processing o Methylation of the 2 OH of the first nucleotide may also occur o The hypothesis The methylation of the 2 OH on these nucleotides may regulate RNA stability potentially affecting translation and RNA processing RNA Capping and Polyadenylation o Polyadenylation occurs polyA in two steps for polyA Cleavage of RNA at specific site often AAUAA creating open 3 end AAUAA is the specific site of cleavage signals that there s a site The addition of multiple 150 250 A s and sometimes U s as well by just upstream that needs to be cleaved polyadenylate polymerase o Polyadenylation serves to Protect RNA from digestion by RNAses Aid in transcription termination proteins involved in RNA cleavage bind Proteins involved in cleavage are also bound to RNA polymerase to RNA polymerase to signal for termination II and other proteins involved in termination o PolyA binding protein is used in nuclear export involved in translation o Polyadenylation can occur before or after termination In Eukaryotes Protein Coding Genes Are Interrupted by Noncoding Sequences Called Introns o Introns are usually spliced out o Introns are interspersed between the exons o Typically introns in humans are on average 3kbp while exons are usually 100 200bp Intron size ranges span 1bp to 10 000bp Not every human gene possesses introns some have many o Introns may harbor long non coding RNAs ncRNAs which may inhibit transcription of certain mRNAs by binding to RNA Also involved in epigenetic regulation mRNA binding to ncRNA gets degraded inhibits translation ncRNA and DNA inhibit transcription Introns Are Removed From Pre mRNAs by RNA Splicing o Intron splicing occurs either during transcriptional elongation and or after termination 1 o Small nuclear ribonucleoproteins snRNPs composed of small nuclear RNAs snRNAs and proteins Recognize 5 and 3 ends of introns and splice them out RNA is splicing catalyst ribozyme snRNPs make up the splicesome o After splicing 5 cap addition and 3 polyadenylation the mRNA goes from being termed as a pre mRNA to a mature mRNA or just mRNA After all three things are completed mature mRNA o Spliceosome Molecular machine that excises introns Consists of snRNPs which bind via proteins and RNA snRNP U1 binds to the 5 splice site and the snRNP bind to the U2 lariat branch point Additional snRNPs bind to U1 and U2 and the spliceosome is formed In a transesterification reaction the lariat is formed and then a second reaction allows the joining of the 3 end of exon 1 and 5 end of exon 2 o Termination occurs when polymerase finds termination site and other o snRNPs protein factor signaling allows for termination Bind to the sequence in a specific manner via the RNA When SN1 binds 5 splice site other snRNPs come in to form the spliceosome Alternative Splicing o Occurs in 95 of multi exonic genes o Spliceosome is regulated by the binding of exonic and intronic splicing enhancers ESEs and ISEs or silencers ESSs and ISSs Nuclear sequences Activator enhancing regions Repressor silencing regions o These proteins cause the spliceosome to bind at various sites allowing the o Enhancer Silencer sequences determine where the spliceosome goes not incorporation of different exons in various transcripts proteins Proteins will bind silencing enhancing regions work with spliceosome or against it Mature Eukaryotic mRNAs Are Exported form the Nucleus 2 o mRNAs are transported out of the nucleus via pores in the nuclear envelope known as nuclear pore complexes NPCs tRNAs are transported as well This happens after RNA processing steps Capping Splicing Polyadenylation If these three things don t go as planned will not be exported o Transcription factors and other proteins such as DNA polymerases RNA polymerases and histone and ribosomal proteins are shuttled into the nucleus via the NPC These can come in through a different pore o Larger molecules proteins RNAs are actively transported across the envelope through NPCs Further Elaboration on Nuclear mRNA Export o Along with polyA binding protein the cap binding protein and the exon junction complex bind to the mature mRNA has occurred The exon junction complex proteins are added after an intron splicing o Nuclear transport receptor proteins then guide mRNA through nuclear pore o mRNA in the cytosol will shed these proteins but they all have an effect on complex NPC the initiation of translation o mRNA coming out of nucleus o Has number of proteins on it polyA binding proteins o Cap binding protein o Cap binding protein exon junction complex and poly A binding protein o Complex of proteins Will interact with a ribosome Protein in NPC allows entity to be shuttled out All involved in exportation and translation Aids in the transportation of mRNA and provides signal Exon junction complex will signal to enzymes that can degrade RNA if This is one of the last steps in degrading improperly formed RNA its not made right mRNA Molecules Are Eventually Degraded in the Cytosol o Half life determined by sequence particularly the 3 untranslated region 3 UTR Not part of the transcript that will be translated Sequence governs structure which governs what can bind to it o 3 UTR is between the 3 of the coding sequence and the polyA tail o The more open a structure the more likely a miRNA will bind to it o mRNAs are degraded by RNAses in cytoplasm The Earliest Cells May Have Had Introns in Their Genes o Introns early hypothesis 3 o Introns late hypothesis accepted the most Introns occurred early in biological evolution and were shed by some organisms prokaryotes Introns are a recent evolutionary strategy found mostly in eukaryotes required for such advanced mechanisms as exon shuffling Exon shuffling two or more exons from different genes are combined after a crossing over event Not common but possible happens in humans o Other hypotheses suggest that introns started out as parasitic elements capable of invading genomes and being replicated using the host s molecular machinery o Organisms that replicated faster have less introns usually An mRNA Sequence is Decoded in Sets of Three Nucleotides o Codons three ribonucleotides in a row Not universal viruses not even inside us In vertebrate mitochondria AGA and AGG are also stop codons but not UGA which codes for tryptophan instead AUA