Study Questions Set 9 Flashcards

1
Q

Briefly explain transport through the nuclear pore

A

POST TRANSCRIPTIONAL CONTROL MECHANISM
• nuclear envelope is perforated by pores that can selectively transport macromolecules across the membrane; only functional mRNAs are exported
• recognizes only 5’ cap before transported; nuclear mRNPs are exported with mRNAs
• may also be linked to splicing (prevents unspliced mRNA from being transported)
• e.g., HIV virus is only exported to cytoplasm if fully spliced

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2
Q

Briefly explain localization of mRNA to specific regions

A

POST TRANSCRIPTIONAL CONTROL MECHANISM
• use cytoskeleton to position mRNA close to sites where protein proceed by mRNA is required
• transport to specific regions involves specific RNA binding proteins
• e.g., mRNAs in learning and memory; localization of beta-actin mRNA to the leading edge of fibroblasts

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3
Q

Briefly explain RNA-editing; alteration of mRNA sequence

A

POST TRANSCRIPTIONAL CONTROL MECHANISM
n protozoans: addition or deletion of U-residues, causes changes to many nucleotides; directed by small guide RNAs (gRNA)  enzyme cascade
• in mammals: site-specific single nucleotide changes; deamination of A to I (inosine), C to U
• e.g., C to U in intestine mRNA causes codon to change into stop codon, resulting in shorter Apo protein

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4
Q

Briefly explain gene silencing by small RNA molecules (siRNA or miRNA)

A

POST TRANSCRIPTIONAL CONTROL MECHANISM
• RNA interference – ability of small, double or single stranded RNA molecules to induce sequence specific gene silencing in complementary regions
• involved in regulation of expression of endogenous genes (for development/differentiation), defense against viral infection, suppression of transposon mobilization, etc.
• e.g., larval protein in C. elegans only translated in early development; mRNA still present later in development but untranslated due to lin4 small RNAs that silence genes

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5
Q

Briefly explain translational control switch

A

POST TRANSCRIPTIONAL CONTROL MECHANISM
• opposing regulation of two coordinated products with single control element that is sensitive to certain environmental conditions
• e.g., ferritin (Fe storage protein) and transferrin receptor (responsible for transport of Fe into cell) are coordinated by IRE element that binds iron-responsive binding protein; when iron is low in the cell, IRE-BP binds to elements, preventing translation of ferritin mRNA so Fe is not stored and preventing degradation of transferrin product to bring Fe into cell)

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6
Q

Briefly explain RNA stability (degradation and stabilization)

A

POST TRANSCRIPTIONAL CONTROL MECHANISM
• balance of degradation and synthesis determines the level of individual mRNAs in cells
• stabilizing elements and instability elements in 3’UTR and in coding sequence
• e.g., maternal mRNA Hsp30 is not detectable until after mid-tailbud stage

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7
Q

Explain the role of mRNA stability in control of gene expression

A
  • balance between mRNA degradation and synthesis determines level of individual mRNA in cells
  • presence of stabilizing elements in 3’UTR and coding sequence
  • instability elements (predominantly found in 3’UTR) usually determines the rate of degradation by interacting with specific RNA binding proteins
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8
Q

Explain the role of RNA editing in control of gene expression

A
  • changes to nucleotide sequence are directed by gRNA; can be large-scale or single nucleotide change
  • changes will produce different product or not produce product at all
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9
Q

Explain the role of iRNA in control of gene expression

A
  • RNA interference induces gene silencing

* can prevent the formation of viruses, prevention of mRNA into protein, etc.

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10
Q

Explain the role of transcriptional control switch in control of gene expression

A

• control element either prevents degradation or translation of mRNA product, controlled by environmental conditions

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11
Q

Explain the role of mRNA localization in control of gene expression

A

• localization of mRNA allows for certain protein product to be in high or low concentration in certain region

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12
Q

Explain the connection between pre m-RNA splicing and transport of mRNA from the nucleus.

A
  • pre-mRNA splicing includes addition of 5’ cap; 5’ cap is recognized by transport machinery (embedded in nuclear membrane)
  • special proteins that recognize processed mRNA attach (likely involved in transport membrane molecule recognition as well); get replaced by cytoplasmic mRNP as it travels through membrane
  • cell has system that prevents the exit of unspliced mRNA
    o proof: HIV makes only a few mRNAs that get fully spliced
    o one includes REV mRNA (reverse transcriptase enzyme) that goes back into the nucleus and helps transport unspliced/unprocessed mRNA across nuclear membrane
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13
Q

What is trans-splicing? Give an example.

A
  • construction of mRNA by splicing of separate RNA molecules, joining the exon of one gene with the exon of another
  • e.g., in Trypanosoma:
    o have leader sequences that give rise to leader exons (which get capped, but not processed at their 3’ ends)
    o also have coding regions for polycistronic primary transcripts (no introns)
     these get spliced into exons that code for protein; leader exons + primary transcripts = transplicing + polyadenylation of 3’ end
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14
Q

What does S in 16S stand for? What is the numerical value of this constant?

A
  • S stands for Svedverg units, which is a measure of sedimentation rate (velocity) of suspended particles when centrifuged under constant conditions; velocity depends on both size and shape of the particle
  • good measure of relative size (units are not additive)
  • 1 S = 10-13 s
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15
Q

What are the roles of three major RNAs in protein synthesis?

A
  • mRNA – carries genetic information from DNA in the form of “codons”
  • tRNA – translates mRNA code; each amino acid has its own tRNA
  • rRNA – associates with proteins to form ribosomes which catalyze the assembly of protein chains
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16
Q

How many different tRNAs are there in a eukaryotic cell? How many different aminoacyl tRNA synthetasis are there in a eukaryotic cell?

A
  • around 50 different tRNAs in animals and plants

- there are 20 different aminoacyl tRNA synthetases (one for each of the amino acids)

17
Q

What are the roles of tRNA in translation?

A
    1. to be linked to a particular amino acid (brings amino acid)
    1. to recognize codon in mRNA so that corresponding AA can be added
  • transfers amino acid from surrounding cytoplasm to corresponding order in amino acid sequence, where anti-codon base pairs with codon; 3’ terminal site fits specifically to amino acid that corresponds with anticodon’s codon
18
Q

What is the wobble position for an anticodon? For a codon?

A
  • wobble position is non-standard pairing in tRNA
  • for a codon, wobble position in the 3rd position
  • for an anti-codon, wobble position in 1st position
19
Q

Explain what does it mean when we say that the code is degenerate? Codons are synonymous?

A
  • code is degenerate because there is more than one codon corresponding to an amino acid (64 codons for 20 aa’s)
  • synonymous codons are codons that code for the same amino acid (typically differ in nucleotides at the third position)
20
Q

How are ribosomal subunits held together? What could be used to separate subunits?

A
  • by divalent cations (e.g., Mg)

- EDTA and high salt concentrations cause the ribosomal subunits to dissociate