| what's 3′ untranslated region (UTR) and 5′ untranslated region (UTR) ? | -3′ untranslated region (UTR) – The untranslated sequence downstream from the coding region of an mRNA.
-5′ untranslated region (UTR) – The untranslated sequence upstream from the coding region of an mRNA. |
| what's a stem-loop? | A secondary structure that appears in RNAs consisting of a base-paired region (stem) and a terminal loop of single-stranded RNA.
Both are variable in size. |
| mRNA instability is due to what? | is due to the action of ribonucleases.
Ribonucleases differ in their substrate preference and mode of attack. |
| what are endoribonuclease and exoribonuclease? | endoribonuclease – A ribonuclease that cleaves an RNA at an internal site(s).
exoribonuclease – A ribonuclease that removes terminal ribonucleotides from RNA. |
| what are processive (nuclease) and distributive (nuclease) ? | processive (nuclease) – An enzyme that remains associated with the substrate while catalyzing the sequential removal of nucleotides.
distributive (nuclease) – An enzyme that catalyzes the removal of only one or a few nucleotides before dissociating from the substrate.
mRNAs exhibit a wide range of half-lives. |
| what's mRNA decay ? | mRNA degradation, assuming that the degradation process is stochastic.
Differential mRNA stability is an important contributor to mRNA abundance and therefore the spectrum of proteins made in a cell. |
| what's the steady state (molecular concentration) ? | The concentration of population of molecules when the rates of synthesis and degradation are constant. |
| why do mRNAs Exist in the Form of mRNPs from Their Birth to Their Death ? | -mRNA associates with a changing population of proteins during its nuclear maturation and cytoplasmic life.
-Some nuclear-acquired mRNP proteins have roles in the cytoplasm.
-A very large number of RNA-binding proteins (RBPs) exist, most of which remain uncharacterized.
-Different mRNAs are associated with distinct, but overlapping, sets of regulatory proteins, creating RNA regulons. |
| what's polyribosome (or polysome) and monocistronic mRNA ? | polyribosome (or polysome) – An mRNA that is simultaneously being translated by multiple ribosomes.
monocistronic mRNA – mRNA that codes for one polypeptide. |
| what's Prokaryotic mRNA Degradation involving multiple enzymes? | Degradation of bacterial mRNAs is initiated by removal of a pyrophosphate from the 5′ terminus.
Monophosphorylated mRNAs are degraded during translation in a two-step cycle involving endonucleolytic cleavages, followed by 3′ to 5′ digestion of the resulting fragments.
3′ polyadenylation can facilitate the degradation of mRNA fragments containing secondary structure. |
| what's poly(A)? and what's poly(A)polymerase (PAP) and poly(A) binding protein (PABP) ? | -poly(A) – A stretch of adenylic acid that is added to the 3′ end of mRNA following its synthesis.
The main degradation enzymes work as a complex called the degradosome.
-poly(A) polymerase (PAP) – The enzyme that adds the stretch of polyadenylic acid to the 3′ end of eukaryotic mRNA.
It does not use a template.
The modifications at both ends of mRNA protect it against degradation by exonucleases.
poly(A) binding protein (PABP) – The protein that binds to the 3′ stretch of poly(A) on a eukaryotic mRNA. |
| what are the two major decay pathways initiated by? | initiated by deadenylation catalyzed by poly(A) nucleases.
Deadenylation may be followed either by decapping and 5′ to 3′ exonuclease digestion, or by 3′ to 5′ exonuclease digestion. |
| what is the decapping enzyme ? cytoplasmic cap-binding protein ? | -The decapping enzyme competes with the translation initiation complex for 5′ cap binding.
-cytoplasmic cap-binding protein – A component of the eukaryotic initiation factor 4F (eIF4F) that binds the 7-methyl guanosine cap at the 5′ end of eukaryotic mRNA |
| what's an exosome? | catalyzes 3′ to 5′ mRNA digestion, is a large, evolutionarily conserved complex. |
| Degradation may occur within what particles? | cytoplasmic particles called processing bodies (PBs).
A variety of particles containing translationally repressed mRNAs exist in different cell types. |
| what are other degradation pathways? | -Four additional degradation pathways involve regulated degradation of specific mRNAs.
-Deadenylation-independent decapping proceeds in the presence of a long poly(A) tail.
-The degradation of the nonpolyadenylated histone mRNAs is initiated by 3′ addition of a poly(U) tail.
-Degradation of some mRNAs may be initiated by sequence-specific or structure-specific endonucleolytic cleavage.
-An unknown number of mRNAs are targets for degradation or translational repression by microRNAs (miRNAs). |
| what are Destabilizing elements (DEs) ? | Specific cis-elements in an mRNA affect its rate of degradation.
Destabilizing elements (DEs) can accelerate mRNA decay, while stabilizing elements (SEs) can reduce it. |
| what are AU-rich elements (AREs) and iron-response element (IRE) ? | AU-rich elements (AREs) are common destabilizing elements in mammals, and are bound by a variety of proteins.
Some DE-binding proteins interact with components of the decay machinery and probably recruit them for degradation.
Stabilizing elements occur on some highly stable mRNAs.
iron-response element (IRE) – A cis sequence found in certain mRNAs whose stability or translation is regulated by cellular iron concentration.
mRNA degradation rates can be altered in response to a variety of signals. |
| what are Aberrant nuclear RNAs are identified and destroyed by ? | RNA surveillance system.
The nuclear exosome functions both in the processing of normal substrate RNAs and in the destruction of aberrant RNAs.
The yeast TRAMP complex recruits the exosome to aberrant RNAs and facilitates its 3′ to 5′ exonuclease activity. |
| what's a oligo(A) tail ? | oligo(A) tail – a short poly(A) tail, generally referring to a stretch of less than 15 adenylates.
Substrates for TRAMP-exosome degradation include unspliced or aberrantly spliced pre-mRNAs and improperly terminated RNA Pol II transcripts lacking a poly(A) tail. |
| what are unstable transcripts (CUTs) ? | The majority of RNA Pol II transcripts may be cryptic unstable transcripts (CUTs) that are rapidly destroyed in the nucleus. |
| what's release factor (RF) and Nonsense-mediated decay (NMD) ? | release factor (RF) – A protein required to terminate polypeptide translation to cause release of the completed polypeptide chain and the ribosome from mRNA.
Nonsense-mediated decay (NMD) targets mRNAs with premature stop codons.
Targeting of NMD substrates requires a conserved set of Upf and SMG proteins. |
| what happens at exon junction complexes (EJC) in mammals? what's the pioneer round of translation ? | -Recognition of a termination codon as premature involves unusual 3′ UTR structure or length in many organisms and the presence of downstream exon junction complexes (EJC) in mammals.
-pioneer round of translation – The first translation event for a newly synthesized and exported mRNA. |
| what's the Quality Control of mRNA Translation Is Performed by Cytoplasmic Surveillance Systems? | -Nonstop decay (NSD) targets mRNAs lacking an in-frame termination codon and requires a conserved set of SKI proteins.
-No-go decay (NGD) targets mRNAs with stalled ribosomes in their coding regions. |
| what does the Localization of mRNAs serves ? what are mRNP granules ? | -diverse functions in single cells and developing embryos.
-mRNP granules – Large mRNA-containing cytoplasmic particles, such as processing bodies (P bodies), stress granules, and neuronal granules. |
| what are the Translationally Silenced mRNAs Are Sequestered in a Variety of RNA Granules? | RNA granules are formed by aggregation of translationally silenced mRNA and many different proteins.
Germ cell granules and neuronal granules function in translational repression and transport. |
| what are Processing bodies (PBs) and Stress granules (SGs) ? | -Processing bodies (PBs) containing mRNA decay components are present in most or all cells.
-Stress granules (SGs) accumulate in response to stress-induced inhibition of translation. |
| what's the perps of mRNAs that are Localized to Specific Regions of a Cell? | -Localization of mRNAs serves diverse functions in single cells and developing embryos.
-Three mechanisms for the localization of mRNA have been documented.
-Localization requires cis-elements on the target mRNA and trans-factors to mediate the localization. |
| what are zipcode (or localization signal) ? | -zipcode (or localization signal) – Any of the number of mRNA cis elements involved in directing cellular localization.
-The predominant active transport mechanism involves the directed movement of mRNPs along cytoskeletal tracks. |
