Term
| Post-transcriptional modifications that occur in the nucleus |
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Definition
| pre-mRNA splicing, poly(A) additon, 5' capping, |
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Term
| Post-transcriptional modifications that occur in the cytoplasm |
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Definition
| de-adenylation and de-capping, translation, precursors cleaved from pre-mRNA |
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Term
| siRNA used in gene knockdown |
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Definition
| siRNA can be designed to inhibit translation of specific mRNAs epxerimentally |
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Term
| correct order of pre-mRNA processing |
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Definition
5’ capping
Cleavage at future poly (A) tail
addition of poly(A) tail
RNA splicing
Mature mRNA |
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Term
| Process of 5' capping (4 steps) |
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Definition
(1) ) Initial step: catalyzed by dimeric capping enzyme which associates with phosphorylated CTD domain of RNA polymerase II
(2) Binding of camping enzyme to CTD focuses capping enzyme on RNAs containing 5’triphosphate
(3) Gamma-phosphate at 5’ end is removed by capping enzyme
(4) ) Separate enzymes transfer methyl groups from S-adenosylmethionine to the N7 position of the guanine and one or two 2’ oxygen’s of the ribose’s at the 5’ end of the nascent RNA |
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Term
| Prokaryotic pre-mRNA modifications |
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Definition
| Prokaryotes have a semi 5' cap consisting of a triphosphate on the 5' end |
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Term
| cellular function of the 5’-cap of eukaryotic mRNA |
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Definition
| o Marks RNA molecules as mRNA precursors and protects them from RNA-digesting enzymes in the nucleus and cytoplasm |
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Term
| the relationship between the cap and the C-terminal domain of RNA Pol II? |
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Definition
| The capping enzyme associates with the CTD of RNA pol II |
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Term
| What types of RNA constitute “pre-mRNA”? |
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Definition
| nascent RNA transcripts from protein coding genes and intermediates of mRNA processing |
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Term
| set of nuclear proteins which pre-mRNA associate with |
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Definition
Heterogeneous ribonucleoprotein particles = hnRNPs
Contain heterogeneous nuclear RNA (hnRNA) = collective term referring to pre-mRNA and other nuclear RNAs of various sizes |
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Term
| functions of hnRNP proteins (4) |
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Definition
Contribute to further steps in RNA processing: splicing, polyadenylation, and export through nuclear pore complexes to the cytoplasm
Association of pre-mRNAs with hnRNP prevents the pre-mRNAs from forming short secondary structures
association of specific sites in pre-mRNA with specific hnRNPs specify RNA splicing, cleavage or adenylation
Some hnRNPs remain localized in the nucleus= function in transport of mRNA |
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Term
| conserved RNA-binding motifs found in hnRNP proteins |
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Definition
| RNA recognition motif, KH motif and RGG box |
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Term
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Definition
| Contains four-standard beta sheets flanked on one side by two alpha helices |
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Term
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Definition
| Three stranded beta sheet supported from one side by two alpha helices. RNA binds to the KH domain by interacting with a hydrophobic surface formed by the alpha helices and one beta strand |
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Term
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Definition
| Contains five (arg-gly-gly =RGG) repeats with several interspersed aromatic amino acids |
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Term
| organic chemistry reaction that is a major component of mRNA splicing |
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Definition
| 2 transesterification reactions |
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Term
| first transesterification reaction |
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Definition
| ester bond between the 5’ phosphorus of the intron and the 3’ oxygen of exon 1 is exchanged for an ester bond with the 2’ oxygen of the branch site |
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Term
| second transesterification reaction |
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Definition
| ester bond between the 5’ phosphorus of exon 2 and the 3’ oxygen of the intron is exchanged for an ester bond with the 3’ oxygen of exon 1, releasing the intron and joining the exons |
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Term
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Definition
| large ribonucleoprotein complex assembled on pre-mRNA |
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Term
| What is the splicesome made of? |
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Definition
170 proteins, 100 splicing factors
Proteins associated with the five snRNPs |
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Term
| relationship of RNA splicing and the SR protein in the inherited childhood disease Spinal Muscular Atrophy. |
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Definition
Mutation that interfere with the binding of an SR proteins to an exonic splicing enhancer prevents formation of the cross-exon recognition complex
Exon is skipped and mRNA is truncated and translated into a mutant protein which causes spinal muscular atrophy |
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Term
| the two types of self-splicing introns |
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Definition
Group I introns present in nuclear rRNA genes of protozoan’s
Group II introns present in protein–coding genes and some rRNA and tRNA genes in mitochondria and chloroplasts of plants and fungi |
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Term
| relationship between 3’ cleavage and polyadenylation |
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Definition
A residues are added to a 3’ hydroxyl generated by an endonucleoytic cleaves of a longer transcript
Requirement of PAP binding links cleavage and polyadenylation, so that the free 3’ end generated is rapidly polyadenylated and no essential information is lost to exonuclease degradation of the unprotected 3’ end |
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Term
| the fate of RNA that is processed out of pre-mRNA |
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Definition
| o Degraded by nuclear exoribonucleases that hydrolyze one base at a time from either the 5’ or 3’ end of an RNA strand |
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Term
| general process by which processed mRNA moves from the nucleus to the cytoplasm |
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Definition
| They transverse the nuclear envelope through nuclear pores |
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Term
| Nuclear Pore Complex (NPCs) |
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Definition
| large, symmetrical structures composed of multiple copies of approximately 30 different nucleoproteins |
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Term
| Which mRNA can travel out of the nucleus |
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Definition
| mRNPs are transported through the NPC via mRNP exporters |
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Term
| how is processed mature mRNA is distinguished from pre-mRNA |
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Definition
| Mature mRNA which can leave the nucleus have poly(A) tails and 5’ caps. They are spliced and do not contain introns. They are unbound to snRNPs |
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Term
| defects in splicing that lead to the symptoms observed in Thalassemia |
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Definition
| Due to mutations in globin-gene splice sites that decrease the efficiency of splicing but do not prevent association of pre-mRNAs with snRNPs. Unspliced globulin pre-RNAs are retained in reticulocyte nuclei and rapidly degraded |
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Term
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Definition
| regulates proper level of translation of multiple mRNAs |
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Term
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Definition
| causes degradation of specific target mRNAs |
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Term
| how RNA interference induces degradation of precisely complementary mRNA |
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Definition
| siRNA base-pairs extensively with its target RNA and induces its cleavage due to argonaute protein. argonaute cleaves the phosphodiester bond of the target RNA across from nucleotides 10 and 11 on the siRNA. RNA is released and degraded by exosomes |
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Term
| Where does iRNA take place? |
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Definition
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Term
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Definition
| RNA-induced silencing complex: contains a single-stranded mature miRNA bound by a multidomain Argonaute protein. Binding of RISC complexes to an mRNA inhibits translation |
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Term
| What cellular process does the poly adenylation of mRNA promote? |
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Definition
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Term
| the cytoplasmic mechanisms, which promote mRNA degradation (3) |
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Definition
Deadenylation-dependent pathway
Deadenylation-independent decapping pathway
Endonucleoytic pathway |
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Term
| Deadenylation-dependent pathway |
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Definition
| length of the poly(A) tail gradually decreases with time through the action of a deadenylating nuclease |
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Term
| Deadenylation-independent decapping pathway |
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Definition
| certain sequences at the 5’ end make the cap sensitive to decapping enzyme |
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Term
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Definition
| does not involve decapping or deadenylation. Does involve RNA interface- each siRNA-RISC complex can degrade targeted RNA molecules, fragments generated by internal cleavage are degraded by exonucleases |
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Term
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Definition
| TOR pathway stimulates the overall rate of protein synthesis by phosphorylating two critical proteins that regulate translation directly. The pathway also activates transcription factors that control expression of ribosomal components, tRNAs, and translation factors, further activation protein synthesis and cell growth |
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Term
| the relationship between the mTOR pathway and the disease tuberous sclerosis complex |
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Definition
| a mutation causes inactivation of regulation factors of mTOR. mTOR pathway runs at high, unregulated levels. these mutations are common in cancer and contribute to cell growth and replication in the absence of normal signals for growth and proliferation |
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Term
| regulation of ferritin mRNA and how it is sensitive to iron levels |
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Definition
| IRE-BP recognizes five specific base in the IRE loop |
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Term
| At low concentrations of iron... |
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Definition
| iron IRE-BP (iron response element binding protein) is in its active form and binds to IREs (iron response elements on ferritin mRNA 5’ UTRs) which inhibits ferritin translation. Low ferritin means less iron is complexed too it, and more iron is available to iron-requiring enzymes |
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Term
| at high concentrations of iron... |
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Definition
| IRE-BP is inactive and translation can proceed |
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Term
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Definition
| o A mechanism of mRNA surveillance which causes degradation of mRNA in which one ore more exons have been incorrectly spliced |
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Term
| The consensus sequence for poly(A) addition is |
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Definition
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Term
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Definition
Poly(A) tails
Introns
A 3’ UTR |
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Term
| Which of the following cis and trans elements function together in a biological process? |
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Definition
Nut and N
AAUAAA and CPSF
TAR and TAT |
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Term
| Which process involves two transesterification reactions? |
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Definition
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Term
| Splice sites in pre-mRNA are marked by two universally conserved sequences contained |
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Definition
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Term
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Definition
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Term
| Indicate the order in which the following steps occur in the production of a mature mRNA |
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Definition
| initiation of transcription, addition of 5´ cap, addition of poly(A) tail, splicing, transport to cytoplasm |
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Term
| Components of the spliceosome include |
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Definition
| proteins that react immunologically with the sera of patients with systemic lupus erythematosus |
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Term
| This type of RNA functions in the removal of introns from pre-RNAs |
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Definition
| snRNA (small nuclear RNA) |
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Term
| Which of these events does not occur within the nucleus? |
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Definition
| RNA editing in protazoans |
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Term
| Which events do occur within the nuclaus? |
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Definition
| capping, adenylation and mRNA editing in eukaryotes |
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Term
| Which type of RNA participates in nuclear export of mRNA? |
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Definition
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Term
| transport of unspliced HIV mRNA from the nucleus to the cytoplasm of host cells is promoted by a virus-encoded protein named |
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Definition
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Term
| microRNAs play a key role in which of the following? |
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Definition
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Term
| Which of the following can affect the cytoplasmic location of mRNAs (3) |
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Definition
the cytoskeleton
cytochalain B
polyribosomes |
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Term
| Which of the following does not part in the degradation process of eukaryotic mRNAs? |
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Definition
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Term
| A ribozyme is an RNA sequence (3) |
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Definition
Uses Mg2+ as a cofactor
Contained in the splicesome
Cataylic RNA that can cleave |
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