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| Question | Answer |
| Name the 8 posttranscriptional regulation pathways | 1. Attenuation 2. Alternative splicing 3. mRNA cleavage 4. RNA Editing 5. Nuclear transport 6. Localization 7. Translational control 8. mRNA stability |
| Define the action of attentuation | Attenuation terminates transcription before the gene sequence is complete by forming alternate hairpin secondary structures if transcription pauses upstream. the trp operon is a common example. |
| Define a riboswitch | A riboswitch is an RNA who's function changes dependent on whether it's bound to a particular small molecule which is in turn dependent on that molecule's concentration in the cell. |
| What are the 5 patterns of alternative splicing? | 1. Exon skipping 2. Intron retention 3. Alternative 5' splice site 4. Alternative 3' splice site 5. Mutually exclusive exons |
| Which nucleotides undergo conversion during RNA editing in mammals | A is edited to I by the ADAR enzyme C is edited to U |
| What are the 3 methods of cytoplasmic RNA localization | 1. Direct Transport 2. Trapping after random diffusion 3. Local trapping with protection and general degredation |
| Localization signals are typically in which area of the mRNA? | 3' Untranslated region (UTR) |
| How is translational control accomplished? | Repressor proteins block the Shine-Dalgarno sequence or the AUG start codon. This is done either via a riboswitch or an antisense RNA |
| How is global transational repression activated? | eIF2 is phosphorylated |
| Define Leaky scanning | When an earlier AUG region is not a good match to the consensus sequence, it will sometimes be skipped during scanning. This allows several versions of the same protein with different 5' ends. |
| How long are mRNA stable in bacteria vs eukaryotes? | several minutes in bacteria 30-600 minute half lives in eukaryotes |
| What are the 2 mechanisms of mRNA degredation? | 1. decaping followed by rapid 5' to 3' degredation 2. gradual poly-A shortening that eventually eats into the coding region of the protein |
| This large complex destroys RNAs | P-body |
| What is the most common function of small non-coding RNA? | Most Small Non-Coding RNAs regulate gene expression via RNA interference. |
| What are the 3 classes of sncRNAs? | 1. microRNAs (miRNAs) 2. small interfering RNAs (siRNAs) 3. piwi-interacting RNAs (piRNAs) |
| What is miRNA cropping and where does it occur? | miRNA cropping is the removal of the two ends (including 5' cap and the poly-A tail) from the miRNA This happens inside the nucleus before transport to the cytosol |
| What is miRNA dicing and where does it occur? | Dicing is the cleavage of the loop end of the miRNA leaving 2 single stranded RNAs This happens in the cytosol. One strand is degraded while the other is bound by Argonaute and other proteins to create an RISC |
| Define RISC | RNA Induced Silencing Complex When these miRNAs match to mRNA they repress translation and eventually encourage degredation. extensive matches to mRNA cause "slicing" of the mRNA which is then rapidly degraded. |
| What is slicing and where does it occur | Slicing is cleavage of mRNA due to an extensive match with an miRNA. This happens in the cytosol. |
| What type of structure does an miRNA gene have? | miRNAs are sets of genes with inverted repeats. They are conserved across species. |
| What is let-7 | let-7 is an miRNA found in worms. |
| What is the function of Drosha RNases? | Drosha RNases releases double stranded RNA (dsRNA) via "cropping". Transforming Primary micro RNA (pri-miRNA) to Precursor micro RNA (pre-miRNA) |
| What are the four proteins in the RISC pathway? | AGO2 VIG FXR Tudor-SN (TSN) These assemble together with the mature miRNA to create the RNA Induced Silencing Complex (RISC) |
| What is the function of AGO2 ? | AGO2 is an RNA helicase. It separates double stranded RNA in the RISC |
| What is the function of Vasa Intronic Gene (VIG)? | Vasa Intronic Gene (VIG) is an RNA binding protein in the RISC |
| What is the function of FXR? | FXR (also, dFXR or Fmr-Fragile X related protein) is an RNA binding protein in the RISC |
| What is the function of Tudor-SN (TSN)? | Tudor-SN (TSN) is a neclease that degrades mRNA as part of the RISC |
| What is RITS? | RNA Induced Transcriptional Silencing (RITS) produces histone and DNA methylation that can silence genes. |
| Define siRNA | Small Interfering RNA (or silencing RNA) is RNA that can target the degradation of specific mRNAs in cells |
| What are the uses of RNAi | RNA Intereference (RNAi) can be used to 1. explore the function of all genes in cultured cells (mass well analysis) 2. suppress genes in a tissue in a specific way. 3. defense mechanism against viruses and transposons |
| Define piRNA | piwi-interacting RNAs (piRNA) block movement of transposable elements in the germ line. Function much like siRNAs to both silence transcription and destroy mRNA. |
| Define the functions of Lnc RNA | Long Non-Coding RNA (lncRNA) 1. provide scaffolding to bring proteins together 2. localize proteins to specific sequences on RNA or DNA. 3. Sometimes act in cis (on same chromosome while connected by an RNA polymerase) sometimes act in trans (act on different chromosome) |
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