Post transcriptional control

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cooxcooxbananas
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188787
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Post transcriptional control
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2012-12-12 00:08:48
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genetics
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genetics
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  1. Transcription control is relatively ______.
    slow
  2. Post transcriptional regulation control is for _______ response to the environment quickly.
    fast
  3. Because _____ is already around, you can use post-transcription.
    mRNA
  4. Using post-transcriptional control can allow you to do what to things?
    • You can change translation of mRNA
    • Change the stability of mRNA
  5. cis elements regulates..
    mRNA
  6. trans factors regulate...
    disfusable factors (Protein/RNA)
  7. If you have too little, or too much fe in the blood what happens?
    death
  8. Too much fe in the blood can cause ____ rxns.
    redox
  9. Fe that is in the blood is bound by...
    transferrin
  10. If cells need iron, what do they do?
    take in iron by transferrin receptors (TFR) on cell membrane
  11. When there is iron in the cell, we either do what two things with it?
    • used
    • stored in a protein called ferritin
  12. High Iron means ____ TFR
    low
  13. High Iron means _____ ferritin
    high
  14. Low TFR means _____ ferritin
    high
  15. Low iron means _____ levels of TFR
    high
  16. Low iron means _____ levels of ferritin
    low
  17. High TFR means _____ levels of ferritin
    low
  18. The changes of iron levels in the bloodstream are ....
    fast
  19. The changes in iron had no effect on .....
    ferritin mRNA levels
  20. What was the experiment regarding regulation of ferritin levels?
    • There was a polysome loading of ferritin mRNA
    • One mRNA with mutiple ribosomes bound
    • If The fe levels were down, the ferritin mRNA on polysomes were down
    • If the fe levels were up, the ferritin mRNA on polysomes were up
  21. Changes in mRNA increases ______ and decreases ______.
    • transcription
    • stability
  22. ferretin protein levels ARE NOT controlled by...
    the abundance of mRNA
  23. Ferritin protein levels are controlled by ...
    cis elements and transfactors
  24. Ferritin does what?
    stores iron and releases it in a controlled fashion.
  25. What are Transferrin receptors needed for?
    to get iron into the cell
  26. What are TFRs (transferrin receptors)
    A carrier protein for transferrin
  27. changes in transcription leads to changes in .....
    RNA
  28. What was the result of the Ferritin RNA abundance expeiriment?
    Turned out it was the same with or without iron ( so RNA doesn't affect it)
  29. When iron was present, the ferritin was ______, meaning lots of polysomal _________ were present, meaning that there was lots of ________.
    • polysomal
    • ribosomes
    • translation
  30. When iron was absent, the ferritin was ______, meaning no polysomal _________ were present, meaning that there was no ________.
    • absent
    • ribosomes
    • translation
  31. What effetcs where ferritin is translated?
    Iron
  32. What is IRE?
    An Iron response element, An RNA sequence that is recognized by the iron regulatory protein.
  33. What is IRP?
    An iron regulatory protein, A translational regulatory protein that recognizes IRE that are found in specific mRNAs.
  34. The IRP may inhibit ______ or stabilize the _______.
    • translation
    • mRNA
  35. What is the 2nd experiment that can be used to help us find where an IRE is located?
    reporter analysis
  36. What is reporter analysis?
    Common reporter w/ green flourescnt protein (GFP)
  37. The reporter analysis is easy to assay because...
    floureses bright green
  38. What is the control of the reporter analysis experiment?
    5'_GFP_UTR__[GFP]__GFP_UTR_3'
  39. 5'_GFP_UTR__[GFP]__GFP_UTR_3'

    the "-" and "+" results for iron was?
    • -Fe = Greenish
    • +Fe = Greenish
  40. 5'_Ferritin__[GFP]__GFP_3'

    the "-" and "+" results for iron was?
    • -Fe = No Green
    • +Fe = Very Green
  41. The iron elements in 5' UTR of ferritin are very....
    responsive
  42. 5'_GFP__[GFP]__Ferritin_3'

    the "-" and "+" results for iron was?
    • -Fe = Greenish
    • +Fe = Greenish
  43. Ferritin 5' UTR has the...
    iron responsive element (IRE)
  44. IRP is a ____ factor
    trans
  45. If you have +Fe, IRP ______ bind to RNA
    can't
  46. If you have -Fe, IRP ______ bind to RNA
    does
  47. When the IRP cannot bind to RNA what occurs?
    translation
  48. When +Fe, ferritin takes the _____up so the cell doesn't die when it takes in the excess iron.
    TFR
  49. The IRP binds______ and is released from the ____, translation occure
    • iron
    • IRE
  50. IRP blocks...
    translation
  51. When iron levels are low, you don't have _________, so you secrete whats left in the cells.
    ferritin
  52. RNA abundance is a balance between ....
    transcription and RNA stability
  53. Absent Fe = ____mRNA
    lots of
  54. Present Fe = ____ TFR mRNA
    a little bit
  55. Transcription of TFR is not Fe _________.
    responsive
  56. TFR mRNA stability is Fe ________.
    responsive
  57. If there is +Fe, the TFR mRNA is ______.
    Unstable
  58. if there is -Fe, the TFR mRNA is _____.
    Stable
  59. If the TFR mRNA is stable, it results in what?
    more Fe being brought into the cells
  60. When using TFR ans GFP to test for iron, what is the control?
    5'_GFP__[GFP]__GFP_3'
  61. 5'_GFP__[GFP]__GFP_3'

    the "-" and "+" results for iron was?
    • -Fe = green
    • +Fe = Green
  62. 5'_TFR__[GFP]__GFP_3'

    the "-" and "+" results for iron was?
    • -Fe = green
    • +Fe = green
  63. 5'_GFP__[GFP]__TFR_3'

    the "-" and "+" results for iron was?
    • -Fe = Green
    • +Fe = Green
  64. If you have no color in the reporter analyses, that means...
    you have no iron
  65. The TFR cis elements are....
    IRE -> 3' UTR
  66. Cis elements and IRE are the same, just in....
    different places
  67. If you have no IRP, the RNA is...
    Not stable
  68. If IRP binds, RNA is ...
    stable
  69. When IRP binds, it makes RNA stable resulting in making more....
    TFR
  70. What has (Fe-S)4 ?
    IRP
  71. When there is +Fe, _____ binds, Fe4-S4, but not RNA.
    IRP
  72. When there is -Fe, IRP _____Fe4-S4, So binds RNA
    has no
  73. Low iron levels affect these how?

    IRP
    ____IRE__Ferretin
    _TFR___IRE____
    • No (Fe-S)4, binds IRE (RNA)
    • No Translation
    • Stabilizes RNA to make more translation
  74. High iron levels affect these how?

    IRP
    ____IRE__Ferretin_
    TFR___IRE____
    • Has (Fe-S)4, cannot bind RNA
    • Translation occurs
    • Destabilizes mRNA, makes less translation
  75. If IRP binds IRE , the iron levels are _____ and the TFR mRNA is ________.
    • Low
    • Stabilized
  76. suppose a person is homozygous for a mutation in the IRP gene that changed the structure of the iron regulatory protein in such a way that it could not bind iron, but it could still bind to IREs. How would this mutation affect the regulation of ferritin?
    This person would be unable to make ferritin, because the IRP would always be bound to the IRE.
  77. suppose a person is homozygous for a mutation in the IRP gene that changed the structure of the iron regulatory protein in such a way that it could not bind iron, but it could still bind to IREs. How would this mutation affect the regulation of transferrin receptor mRNAs?
    The amount of transferrin receptor mRNA would be high, even in the presence of high amounts of iron,because the IRP would always remain bound to the IRE and stabilize the transferrin receptor mRNA.
  78. Suppose a person is homozygous for a mutation in the IRP gene that changed the structure of the iron regulatory protein in such a way that it could not bind iron, but it could still bind to IREs. Do you think such a person would need more iron in his or her diet than normal individuals?
    Such a person would not have any problem taking up iron into his/her cells. In fact, this person would take up a lot of iron via the transferrin receptor, even when the iron concentrations were high.
  79. Suppose a person is homozygous for a mutation in the IRP gene that changed the structure of the iron regulatory protein in such a way that it could not bind iron, but it could still bind to IREs. Do you think that excess iron in the diet would be more toxic than it would be for normal individuals?
    Yes
  80. Why would excess iron in the diet be very toxic?
    • For two reasons. First, the person cannot make ferritin, which prevents the toxic buildup of iron in the cytosol.
    • Second, when iron levels are high, the person would continue to synthesize the transferrin receptor,which functions in the uptake of iron.
  81. What  prevents the toxic buildup of iron in the cytosol?
    ferritin
  82. What are the disadvantages of mRNAs with a short half-life compared with mRNAs with a long half-life?
    A disadvantage of mRNAs with a short half-life is that the cells probably waste a lot of energy making them
  83. What are the advantages of mRNAs with a short half-life compared with mRNAs with a long half-life?
    An advantage of short-lived mRNAs is that the cell can rapidly turn off protein synthesis.
  84. eukaryotic primary transcripts are non-___________.
    functional
  85. mRNA is responsible for...
    Coding, so that things can be translated.
  86. RNAPII consists of
    mRNA
  87. Promoters are transcribed at the ...
    interior promoters of tRNAs in RNAPIII (5s rRNA)
  88. RNAP II consists of (specifically)
    • U-RNAs
    • miRNA (micro)
  89. URNAs are U-rich RNAs that consists of what two components?
    • snRNA (small nuclear)
    • snoRNAs (small nucleolar)
  90. snRNA (small nuclear) aids in...
    mRNA splicing
  91. snoRNAs (small nucleolar) aids in
    rRNA modification
  92. what is an miRNA
    a "micro" RNA that is less than 25 nucleotides when mature
  93. What are the three rRNA operons that lead to maturation.
    • 18S
    • 5.8S
    • 28S
  94. What do RNA operons require for maturation?
    cleavage and modification
  95. What is gRNA?
    RNAs that guide the insertion or deletion of uridine residues into mitochondrial mRNAs by RNA editing
  96. RNA editing is....
    Changes the sequence of the RNA (no longer matches the gene)
  97. Lnc stands for...
    Long non-coding RNA
  98. Lnc RNA is when you have a ...
    non-protein coding that is more than 200 nucleotides when mature
  99. the five steps of mRNA processing
    • 1) Synthesis of the 5' cap
    • 2) Synthesis of the 3' poly-A tail
    • 3) Splicing (removal of useless sequences//Spliced together for an ORF)
    • 4) Base modification (methylation of some A)
    • 5) RNA editing (sequence change of the RNA)
  100. the largest subunit of RNAPII is....
    The CTD
  101. What does CTD stand for?
    Carboxyl terminal domain
  102. What is the CTD (carboxy terminal domain) consists of?
    A capping enzyme, spliceosomal subunits, poly-A polymerase
  103. What is the function of the CTD?
    cappin enzyme, spliceosomal subunits and poly-A polymerase all bind to the CTD and that is how the RNA is recognized
  104. The CTD aids in the recognition of?
    the RNA
  105. What is the heptapeptide?
    A repeating sequence found in CTD sequence
  106. What is the CTD heptapeptide sequence?
    Tyr  Ser(-OH)  Pro  Thr  Ser(-OH)  Pro  Ser(-OH)
  107. heptapeptide can be phosphorylated on the....
    Ser OH group
  108. The RNAII A is not phosphorylated on the....
    CTD
  109. What protects the RNA from being degraded by enzymes that degrade RNA from the 5' end?
    The cap
  110. What are the functions of the poly-A on the mRNA?
    • 1) RNA stability
    • 2) Enhances Translation
  111. there is some _______ between stability and tail length
    correlation
  112. on a histone mRNA there is no...
    Poly-A
  113. The cis element in polyadenelyation is...
    • AAUAAA
    • (A2UA3)
  114. poly A polymerases are...
    trans factors
  115. what are the three steps of poly adeneylation?
    • 1) Cleavage
    • 2) addition of Poly A
    • 3) termination
  116. Polyadenylation does not happen with _______mRNAs
    histone
  117. Polyadenylation does not happen with histone mRNAs
    because they dont have A2UA3
  118. what are the 2 types of transfactors involved in splicing?
    • SR proteins (Ser-Arg rich)
    • snRNPs (small nuclear ribonuclear proteins)
  119. What are the components of the snRNPs (small nuclear ribonuclear proteins)?
    U1, U2, U4/U6, U5 and proteins
  120. transfactors are necessary for specific ________.
    splicing
  121. The average size of exons in humans are...
    about 150 nucleotides (small)
  122. the size of an intron can be....
    small to huge
  123. What are the three steps to exon definition?
    • 1) U1 snRNP binds to 5' splice site
    • 2) U2 snRNP binds to 3' splice site
    • 3) SR proteins bind to U1/U2 snRNPs and coat the exon, making it "defined"
  124. When is an exon defined?
    SR proteins bind to U1/U2 snRNPs and coat the exon
  125. What are the steps to alternative splicing?
    • 1) define exon
    • 2) nucleophilic attack of 2' OH of branch point A on the 3' Phosphate of the 5' exon
  126. A spliceosome consists of...
    SR proteins, snRNPs
  127. what holds RNA fragments together?
    splicesosome
  128. splicing is two...
    transesterifications
  129. What are two types of RNA editing?
    • 1) Substitution editing
    • 2) Insertion/Deletion
  130. Subsititution editing is usually found in...
    humans
  131. Insertion/deletion editing is usually found in...
    parasites
  132. When apoliprotein B is edited by a single C -> U, what happens?
    you get an early stop codon
  133. Short apo B -> ______lipids (_________)
    • exports
    • (edited)
  134. Short apo B -> _______lipids (________)
    • import (liver)
    • (non-edited)
  135. What is alternative splicing?
    In alternative splicing, variation occurs in the pattern of splicing, so the resulting mRNAs contain alternative combinations of exons.
  136. What is its biological significance of alternative splicing?
    The biological significance is that two or more different proteins can beproduced from a single gene.
  137. After the intron (which is in a lariat configuration) is released during pre-mRNA splicing, a brief moment occurs before the two exons are connected to each other. Which snRNP(s) holds the exons in place so they can be covalently connected to each other?
    U5
  138. What are the four step to the splicing of pre-mRNA?
    • 1) U1 binds to 5' splice site, U2 binds to branch site
    • 2) U4/U6 and U5 trimer binds, intron loops out and exons and brought close together
    • 3) 5' splice site is cut, 5' end of intron is connected to the A in the branch site to form a lariat while U1 and U4 are released
    • 4) 3' splice site is cut, Exon are connected, The lariat intron is relased with U2, U5 and U6, intron will be degraded
  139. Explain how you would use a poly-dT column to obtain a purified preparation of mRNA from eukaryotic cells. 7 steps
    • 1) mRNA molecules bind to the column b/c they have a Poly A tail.
    • 2) The A and T hydrogen bond
    • 3) To purify, get a sample of cells and break them open by homogenization
    • 4) remove large cellular structures by centrifuge (structures in pellet, RNA in supernatant)
    • 5) pour high-salt supernatant over poly dT column
    • 6) to break bonds pour low salt concentration over column, to get excess material off.
    • 7) mRNAs will stay due to hydrogen bonding

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