09 - RNA Synthesis and Processing

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09 - RNA Synthesis and Processing
2014-08-22 20:13:13
rna synthesis processing
09 - RNA Synthesis and Processing
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  1. DNA Replication (10,000 ft. Overview)
    Two identical daughter strands are produced from 1 DNA molecule; prerequisite for transmission of genetic material to the progeny of any cell or organism; requires a number of helicases, topoisomerases, and DNA-dependent DNA polymerases
  2. Transcription (10,000 ft. Overview)
    • Process by which a section of DNA 
    • is transferred to RNA; facilitated by DNA-dependent RNA polymerases; tightly regulated by transcription factors; in eukaryotes RNA Pol II synthesizes the primary transcript of mRNA (pre-mRNA), which is processed further for translation (this typically includes addition of a 5’-cap, a poly(A) tail and splicing
  3. Translation (10,000 ft. Overview)
    Process in which mRNA produced by transcription is decoded by rsomes to synthesize a specific AA chain, or PP, that will be further modified and folded into a functional protein
  4. Reverse Transcription (10,000 ft. Overview)
    Transfer of information from an RNA template to DNA; reverse transcriptase creates ssDNA from an RNA template; retroviruses use this mechanism; in eukaryotes telomere synthesis and retro-transposons use this mechanism
  5. RNA Replication (10,000 ft. Overview)
    Process in which RNA is synthesized from an RNA template; all RNA viruses with no DNA stage (polio, hep C, etc.) replicate this way; RNA replicated enzymes are called RNA-dependent RNA polymerases and are found in many eukaryotes where they are involved in RNA silencing
  6. Where is mRNA found?
    Found in the cytoplasm
  7. Where is pre-mRNA found?
    Found only in the nucleus of a eukaryote
  8. What roles do mRNAs, rRNAs, and tRNAs play in protein synthesis?
    mRNA encodes for all proteins, rRNA is the main enzymatic component of rsomes, and tRNA is critical for decoding the nucleotide sequence in AAs of the corresponding protein
  9. what do ncRNAs such as miRNAs do?
    Post-transcriptionally regulate the stability and hence the abundance of protein coding mRNAs; many major cellular functions such as development, differentiation, growth, and metabolism are regulated by miRNAs; gain of function of specific miRNAs (oncomirs) has been associated with certain types of cancer
  10. What is the composition of a rsome?
    Composed of 65% ribosomal RNA and 35% ribosomal proteins
  11. What is a ribozyme?
    An RNA molecule that is capable of catalyzing specific biochemical rxns; similar to the action of protein enzymes
  12. What is TERC?
    This is a RNA component of telomerase that serves as a template for telomere replication (reverse transcription)
  13. What do mutations in TERC cause?
    Autosomal dominant dyskeratosis congenital
  14. What does a spliceosome do?
    This is a large RNA-protein molecular complex which removes introns from transcribed pre-mRNA
  15. What do spliceosomes contain?
    Five small nuclear RNAs (snRNA) and numerous associated proteins
  16. What are snRNPs?
    RNA-protein complexes that combine unmodified pre-mRNA and various other proteins to form a spliceosome
  17. What do mutations in U2 snRNA cause?
    Global disruption of alternative splicing and neurodegeneration
  18. What enzymatic activity does the rRNA in rsomes have?
    Has the catalytic peptidyl transferase activity that links AAs together during protein synthesis
  19. What happens when you have a loss of rRNA modifications?
    Developmental defects, while increased oxidation of 5S rRNA has been associated with Alzheimer’s disease
  20. What does RNase MRP do, and what happens when mutations occur?
    It is a ribozyme that is involved in mitochondrial DNA replication and is a precursor to rRNA processing in the nucleus; mutations in the RNA component of RNase MRP causes cartilage-hair hypoplasia, a pleiotropic human disease
  21. What are some examples of notable human diseases caused by RNA viruses?
    HIV; Hep A and C; Influenza A, B, and C; Dengue virus; West Nile virus
  22. What is the biomedical impact of reverse transcriptase inhibitors?
    Used as therapeutic strategies against AIDS; nucleoside and nucleotide analogs can prevent HIV from reverse transcribing its RNA into DNA, which is an essential step for integration into the host genome during the life cycle of the virus
  23. How much of the total RNA in the cell does mRNA comprise?
    Only about 5%; however, mRNA is the most heterogeneous type in terms of size and sequence
  24. What is the beginning and end of mRNA?
    The life of mRNA begins with transcription and ends with controlled degradation (mRNAs have a precisely defined half-life); mRNA molecules may be processed and transported prior to translation
  25. What are the components of a mature eukaryotic mRNA, and what does each component do?
    • 5’-cap: regulates mRNA stability, nuclear export, and cap-dependent translation; prevents degradation by exonucleases
    • 5’-UTR: untranslated region directly upstream of the initiation codon; it is important for regulation of translation efficiency
    • Coding Sequence: Joined exon sequences (after splicing), which encodes for proteins
    • 3’-UTR: this is an untranslated region immediately following the translation termination codon; this area can contain elements such as hairpin loops that regulate mRNA stability
    • Poly(A) Tail: This is stretch of RNA that has only adenine bases; regulates nuclear export, translation, and stability of mRNA
  26. What are the components of a typical eukaryotic protein coding gene, and what does each component do?
    • Enhancer: this is a DNA sequence that regulates gene expression rate; the enhancer can be located close, far upstream, or even in the intragenic region of the gene
    • Promoter: DNA sequence that regulates gene expression rate; this is located directly upstream of the transcription start site (TSS is between the promoter and 5’-UTR)
    • Exons: these are DNA sequences that encode for the protein coded for by the gene; this is the expressed region which will remain present within the mature mRNA
    • Introns: these are intragenic regions, which are non-coding; they are transcribed but spliced out before translation
    • UTRs: these are untranslated regions at the 3’ and 5’ ends of the transcribed region; plays a regulatory role in mRNA
    • stability and translation
  27. What role does DNA-dependent RNA Polymerase play in the cell?
    RNA Pol (RNAP) is found in all organisms and many viruses; all cellular RNA is synthesized by RNAP based on DNA templates; RNAP does not require a primer and synthesizes RNA de novo; RNAP has no proofreading capability, and has a high error rate
  28. In what direction is RNA synthesis?
    Occurs in the 5’ to 3’ direction (like DNA synthesis)
  29. What are the subunits of the core enzyme of RNAP?
    • Β’: largest subunit; contains part of the active center responsible for RNA synthesis; contains determinants for non-sequence-specific interactions with DNA
    • Β: second-largest subunit; contains the rest of the active center responsible for RNA synthesis; contains determinants for non-sequence-specific interactions with DNA and RNA
    • α: third-largest subunit; present in 2 copies per molecule of RNAP; contains 2 domains: αNTD (N-Terminal domain) contains determinants for assembly of RNAP; αCTD (C-terminal domain) contains determinants for interaction with promoter DNA
    • ω: smallest subunit; facilitates stable assembly of RNAP
  30. What is the σ factor?
    This is a bacterial transcription initiation factor that enables specific binding of RNAP to gene promoters; the specific σ factor used to initiate transcription of a given gene will vary, depending on the gene and the environmental signals needed to express that gene
  31. What is the RNAP holoenzyme?
    The core enzyme and the σ factor together
  32. What does RNA Pol I do in relation to RNA?
    Synthesizes pre-rRNA 45S, which matures into 28S, 18S, and 5.8S rRNAs; these form the major RNA sections of the rsomes
  33. What does RNA Pol II do in relation to RNA?
    Synthesizes precursors of mRNAs and most snRNAs and miRNAs; is strictly controlled by transcription factor binding to promoter sequences
  34. What does RNA Pol III do in relation to RNA?
    Synthesizes tRNAs, 5S rRNA, and other small RNAs found in the nucleus and cytosol
  35. Products of the RNA Pols
  36. What is the biomedical impact of α-Amanitin?
    It binds to the largest subunits of RNAP II and RNAP III; this results in the incorporation of new ribonucleotides into the nascent RNA chains, which halts gene expression; possibly the most deadly of all amatoxins
  37. What is the biomedical impact of Actinomycin D?
    Isolated from soil bacteria Streptomyces; prevents transcript elongation by RNAP; this was the first antibiotic shown to have anti-cancer activity
  38. What is the biomedical impact of Rifampicin?
    Typically used to treat Mycobacterium infections; inhibits bacterial RNA synthesis; blocks RNA synthesis by physically preventing extension of RNA products beyond a length of 2-3 nucleotides
  39. How do resistances to Rifampicin arise?
    Mutations occur that alter the binding site on RNAP; this results in decreased affinity for rifampicin
  40. What are cis-regulatory elements?
    DNA sequences that control the transcription of genes by functioning as binding sites for transcription factors; found in prokaryote transcription
  41. What are trans-regulatory elements?
    DNA sequences encoding for transcription factors; found in prokaryote transcription
  42. What are trans-acting factors?
    Transcription factors that control the expression of other genes by binding to cis-regulatory DNA sequences
  43. What two essential cis-regulatory elements are found on bacterial promoters?
    The -10 bp sequence/Pribnow box and the -35 bp sequence; these are recognized by the RNAP holoenzyme, which is an essential step for initiation of transcription in bacteria
  44. What do the -10/-35 bp sequences and σ factor determine?
    They determine the binding efficacy of RNAP holoenzyme and regulate rate of transcription
  45. What are the steps of RNA transcription in prokaryotes?
    Initiation, elongation, and termination
  46. Initiation of transcription in prokaryotes
    First, the RNAP holoenzyme binds to the promoter; at the start of initiation, the core enzyme is associated with an σ factor that aids in finding the appropriate -35/-10 bp sequences upstream of the TSS; next, after the first bond is synthesized, RNAP must clear the promoters through promoter escape and a transcription elongation complex is formed
  47. What is abortive initiation?
    This is where the RNAP tries to clear the promoter but the RNA transcript is released and truncated transcripts occur; this will continue until an RNA product of a threshold length of approximately 10 nt is synthesized
  48. What happens during elongation?
    The σ factor is released and replaced by NusA; the promoter escapes through a scrunching mechanism, which builds up the energy needed to break interactions between RNAP and the promoter
  49. How does Rho-independent termination occur?
    Also called intrinsic termination; transcription stops when the RNA molecule forms a G-C-rich hairpin loop followed by a run of Us; this produces mechanical stress which breaks the weak rU-dA bonds now filling the DNA-RNA hybrid; this pulls the poly-U transcript out of the active site of the RNAP terminating transcription
  50. How does Rho-dependent termination occur?
    The protein factor “Rho” destabilizes the interaction between the template and mRNA, thus releasing the newly synthesized mRNA from the elongation complex
  51. Transcription
  52. What basic and specific transcription factors are needed to initiate transcription in eukaryotes?
    TATA box found -25 bp; CAAT box found -80 bp; GC box found -100 bp; these support RNAP II
  53. What transcription factors in eukaryotes form a pre-initiation complex?
  54. What is the mediator transcription factor in eukaryotes?
    It is a general transcription factor which helps to guide the pre-initiation complex to the core promoter sequence; it functions as a transcriptional co-activator
  55. What is SAGA?
    It is a multi-protein chromatin modifier
  56. What is TFIID?
    Transcription Factor II D, otherwise known as the TATA-binding protein
  57. What is TFIIH?
    Transcription factor II H; helicase and kinase activity
  58. How does the pre-initiation complex in eukaryotes form?
    • 1. TBP as a subunit of TFIID initiates the assembly of RNAP II at the promoter
    • 2. 5 more transcription factors plus RNAP combine around the TATA box in a series of stages to form the pre-initiation complex
    • 3. TFIIH contains helicase activity and is required to separate the dsDNA to form the initial transcription bubble
  59. How does promoter clearance in eukaryotes occur?
    After several rounds of abortive initiation, promoter clearance is triggered through phosphorylation of RNAP II at the carboxy-terminal domain (CTD) by the kinase in TFIIH, which changes the conformation/activates RNAP and also leads to the recruitment of capping enzyme
  60. What do we know about termination in eukaryotes?
    It involves cleavage of the new transcript followed by polyadenylation at the new 3’ end
  61. In eukaryotes, what modifications does pre-mRNA undergo before becoming mature mRNA?
    Addition of a 7-methylguanosine cap to the 5’ end, 3’-polyadenylation, splicing, and export to the cytoplasm
  62. What is the structure of the 7-methylguanosine cap?
    7-methylguanosine is attached to the 5’ end of almost all eukaryotic and viral mRNAs though a 5’,5’-triphosphate linkage between the m7G cap and the first mRNA nucleotide
  63. What enzymes are involved in the addition of the 5’ cap?
    Synthesis of the cap is carried out by RNA triphosphate, guanylyltransferase, and methyltransferase tethered to the carboxy-terminal domain (CTD) of Pol II; only mRNAs in the nucleus are capped
  64. What is the biomedical impact of viruses capping their mRNAs?
    For efficient translation, to limit degradation by cellular exonucleases, and to avoid recognition as foreign entities; they are often generated through mechanisms different from their host cell, which has been exploited for antiviral drug design
  65. What is polyadenylation?
    Process in which the pre-mRNA is cleaved at its 3’ end and a tail of adenosine monophosphates is added
  66. What binds the cleavage signal sequence?
    An enzyme complex that includes an endonuclease, a polyadenylate polymerase, and several other multi-subunit proteins involved in sequence recognition, stimulation of cleavage, and regulation of the length of the poly(A) tail
  67. What does polyadenylate polymerase do?
    It synthesizes a poly(A) tail 80 to 250 nucleotides long, beginning at the cleavage site
  68. What have defects in polyadenylation
    have been connected to?
    Neonatal diabetes and IPEX (immune dysfunction, polyendocrinopathy, enteropathy, X-linked) and to be associated with type I and II diabetes, preeclampsia, fragile X-associated premature ovarian insufficiency, ectopic Cushing syndrome, and cancer including endocrine tumors
  69. What is alternative splicing?
    It is a mechanism in which certain exons may be included or excluded from the mature mRNA
  70. What does alternative splicing achieve?
    It allows different proteins to be synthesized from one gene only and increases the diversity of proteins encoded by a genome; in humans, most multiexonic genes are alternatively spliced
  71. What is trans-splicing?
    Joins two exons that are originally not within the same RNA transcript
  72. What does a spliceosome do?
    This is how most eukaryotic mRNAs remove introns; it is a complex of snRNPs; the snRNPs recognize intron/exon borders, then the spliceosome catalyzes a cut-and-paste rxn that removes introns and joins exons
  73. What are the intron/exon borders?
    A donor site, a branch site, and an acceptor site
  74. What is self-splicing?
    Occurs for rare introns that form a ribozyme, performing the functions of the spliceosome by itself; there are three types of self-splicing introns, Group I, Group II and Group III
  75. Retinitis Pigmentosa
    Genetic, degenerative eye disease; progressive loss of peripheral and night vision that can lead to total vision loss; 4 of the identified RP genes encode for proteins involved in splicing
  76. Spinal muscular atrophy
    Common autosomal recessive diseases leading to death in childhood; destroys the motor neurons controlling voluntary muscle movement, rendering muscles flaccid and weakened; caused by a mutation in the SMN1; SMN1 is involved in the biogenesis of snRNPs
  77. Beta thalassemia
    Group of genetic blood disorders caused by reduced or absent synthesis of the hemoglobin beta chain; BT is caused by mutations of the splice donor or acceptor sites leading to incorrect splicing of β-globin mRNA; clinical symptoms: asymptomatic to severe anemia
  78. Systemic lupus erythematosus
    • Chronic inflammatory disease where the immune system attacks the tissues and organ systems throughout the body; SLE is triggered by an autoimmune response against snRNPs; it is characterized by autoimmune antibodies directed against snRNPs and Sm proteins.
    • Clinical symptoms: rash (“butterfly rash” occurring on the face); arthritis; muscles aches and more