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Biotechnology I > Ch. 5 Based Technologies > Flashcards

Ch. 5 Based Technologies Flashcards

1
Q

Which of the following statements about antisense RNA is true?

A

All of the above statements are true

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2
Q

Which biological function is not controlled by antisense RNA?

A

Replication of prokaryotic genomic DNA

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3
Q

Which of the following is a modification of antisense oligonucleotide structure to increase intracellular stability?

A

All of the above

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4
Q

How can antisense RNA be expressed within a cell?

A

The target gene can be cloned inversely into a vector and under the control of an inducible promotor

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5
Q

Which of the following terms describes when gene regulation occurs by short is dsRNA molecules triggering an enzymatic reaction that degrades the mRNA of a target gene?

A

All of the above

  • post-transcriptional gene silencing
  • quelling
  • co-suppression
  • RNA interference
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6
Q

Which statements about RNAi is not correct?

A

Non-specific interactions between the antisense siRNA and mRNA often cause mRNAs to be degraded that should not have been

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7
Q

Which of the following is NOT a method for delivering dsRNA or RNAi into Drospholia or C. elegans?

A

Injection of dsRNA into eggs

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8
Q

How can RNAi be triggered in mammalian cells?

A

All of the above

  • transfection of siRNA
  • chemically synthesized siRNA
  • degradation of target mRNA through shRNA creation
  • modification is an existing shRNA to recognize a different mRNA
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9
Q

What information has been obtained through the creation of RNAi libraries?

A

The function of unknown proteins by degrading all of the mRNA for that protein

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10
Q

What is a ribozyme?

A

An RNA molecule that binds to specific targets and catalyzes reactions

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11
Q

Which of the following is a large ribozyme?

A

Twort ribozyme

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12
Q

What process is used to identify possible ribozyme substrates?

A

DNA SELEX

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13
Q

What property must a ribozyme possess in order to be used in clinical medicine?

A

All of the above

  • stability and resistance to degradation
  • no deleterious side effects to the host
  • expression within a diseased cell only
  • be able to be delivered to the correct location
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14
Q

What is a riboswitch?

A

An mRNA sequence that binds directly to an effector molecule to control the translation of the mRNA into protein

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15
Q

Which of the following is NOT an example of an effector molecule for riboswitches?

A

Antisense RNAs

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16
Q

Which RNA is incorrectly paired with its function?

A

piRNA - RNA processing

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17
Q

Which of the following helps replicate telomeres?

A

TERC

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18
Q

In drosophila, two non-coding RNAs called roX1 and roX2 are used to…

A

Idk

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19
Q

What is the role of the alpha antisense form in PTEN expression?

A

Idk

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20
Q

What role do piRNAs play?

A

Idk

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21
Q

snRNA -

A

RNA processing

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22
Q

circRNA -

A

Transcriptional regulation

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23
Q

Xist -

A

Chromosomal structure

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24
Q

lncRNA -

A

Transcriptional regulation

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25
Q

Roles of non coding RNA

A
  • take part in translation; tRNA and rRNA
  • introns splicing: snRNA, snoRNA, gRNA
  • catalyze enzyme reaction; ribozyme
  • genomic integrity
  • protection
  • regulate gene expression
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26
Q

___ is an enzyme that used an RNA component (TERC) to regenerate the ends that are not created during replication, maintaining the chromosome structure.

A

Telomerase

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27
Q

___ ___ ___ contains the active site for DNA synthesis.

A

Telomerase reverse transcriptase (TERT)

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28
Q

Gene dosage compensation

In Drosophila, two noncoding RNAs called roX1 and roX2 complex with five different proteins to form ___ ___.

A

MSL complex

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29
Q

Gene dosage compensation

Which noncoding RNA coats the inactive X chromosome?

A

Xist

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30
Q

Gene dosage compensation

The Xist gene of the active X chromosome is inactivated by ___.

A

Methylation

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31
Q

Piwi-interacting RNAs

The ___ are encoded in genome in large clusters or within introns of other genes.

A

piRNAs

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32
Q

Piwi-interacting RNAs

They are complementary in sequence to ___ ___.

A

Endogenous transposons

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33
Q

Piwi-interacting RNAs

The __ __ binds and cleave any complementary RNA produced by transposon.

A

PIWI complex

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34
Q

Antisense RNA

Transcription uses the antisense strand as a template, resulting in an __.

A

mRNA

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35
Q

___ ___ is synthesized using the sense strand as template.

A

Antisense RNA

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36
Q

___ ___ ___ are complementary to a target mRNA, blocking either protein translation or splicing of introns.

A

Antisense RNA sequences

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37
Q

RNA modulates transcription: antisense RNA

Antisense DNA targets mRNA for ___.

A

Degradation

38
Q

RNA modulates transcription: antisense RNA

The ___ ___ encodes three noncoding RNAs: PTENpg1, asRNA alpha, asRNA beta.

A

PTEN pseudogenes

39
Q

RNA modulates transcription: antisense RNA

The ____ interact with DNMT3A and EZH2 to condense the histones around the PTEN gene.

A

asRNA alpha

40
Q

RNA modulates transcription: antisense RNA

The ___ and ___ prevent the miRNAs from promoting the degradation of normal PTEN mRNA.

A

PTENpg1 and asRNA alpha

41
Q

RNA modulates transcription: antisense RNA

___ ___ are synthesized chemically and injected into a cell to block mRNA translation.

A

Antisense oligonucleotides

42
Q

RNA modulates transcription: antisense RNA

___ ___ are cloned in inverted orientation so that the sense strand is transcribed to yield antisense RNA.

A

Antisense genes

43
Q

The ___ ___ anneals to the normal mRNA, preventing its expression.

A

Antisense RNA

44
Q

Antisense RNA -

A

Backwards compliment of the normal RNA for a target gene

45
Q

Antisense RNA is designed to..

A

Bind the target mRNA and prevent translation

46
Q

Antisense oligonucleotides -

A

Short sequences designed to hybridize with mRNAs and prevent translation

47
Q

___ ___ of cellular proteins can be used to determine if the protein production is reduced.

A

Proteomic analysis

48
Q

The oligonucleotides are susceptible to degradation by ___ ___.

A

Intracellular nuclease

49
Q

First generation therapeutic agents

A
  • modification includes adding sulfur to the phosphodiester backbone
  • the RNA-DNA duplex activates the Rnase H which cleaves hybrid molecules
50
Q

Second generation antisense therapeutic agents

A
  • typically contain alkyl modifications at the 2’ position of the ribose
  • less toxic and more specific than phosphorothioate-modified molecules
51
Q

Third generation antisense oligonucleotides

A
  • contain a variety of modifications within the ribose ring, and/or the phosphate backbone, as well as being less toxic
  • some modifications are made to both enhance stability and facilitate the binding to the target site
52
Q

RNA modulates transcription: antisense RNA

Their use is restricted to __ __ or __ __ __ __ since they are resistant to Rnase H.

A

Splice sites or block ribosome binding sites

53
Q

RNA modulates transcription: antisense RNA

___ ___ with Rnase H-sensitive cores are employed.

A

Chimeric oligonucleotides

54
Q

RNA modulates transcription: antisense RNA

___ ___ ___ are not easily internalized by cells.

___ is often accomplished using liposomes to facilitate cellular uptake.

A

Free antisense oligonucleotides

Delivery

55
Q

Correction of a mutant splice site with an antisense oligonucleotides can be used to treat ___.

A

B-thalassemia

56
Q

RNA modulates transcription: RNA interference

A
  • double-stranded RNA, produced by virus or microRNA from genome, triggers RNA interference
  • dicer recognizes dsRNA and cuts it into 21-23 nucleotides
  • a kinase phosphorylates the 5’ end of each piece
  • RISC unwinds the siRNAs and uses one strand to search out complementary mRNA, which later is cleaved by Argonaut
57
Q

RNA modulates transcription: RNA interference

Amplification of RNAi

A
  • after mRNA is cleaved, RNA-dependent RNA polymerase binds to some of these fragments and synthesized complementary strands
  • dicer recognizes these fragments and creates more siRNA
  • the RISC complex containing the single-stranded siRNA can also recognize and bind to complementary DNA sequence
  • when RISC associates with a repetitive DNA element, various histone-modifying enzymes and silencing complexed are activated
  • the regions become heterochromatin, thus silenced
58
Q

RNA modulates transcription: MicroRNAs

The gene for the miRNA is transcribed into an RNA that folds into a ___ ___.

A

Stem loop

59
Q

RNA modulates transcription: MicroRNAs

___ cleaves pri-miRNA to create pre-miRNA.

A

Drosha

60
Q

RNA modulates transcription: MicroRNAs

In cytoplasm, ___ cuts the end of pre-miRNA to form a mature miRNA.

A

Dicer

61
Q

RNA modulates transcription: MicroRNAs

___ ___ creates the single-stranded template and searches the cytoplasm for any matching sequence.

A

RISC complex

62
Q

Amplification of RNAi for studying gene expression

C. elegans can take up dsRNA by…

A
  • ingesting transgenic bacteria expressing dsRNA
  • bathing in a solution
  • by injection
63
Q

RNAi for studying mammalian genes

RNAi can be triggered in mammalian cells using ___ ___ ___.

A

Chemically synthesized siRNA

64
Q

RNAi for studying mammalian genes

The dsRNA shorter than 30 nucleotides activated the mammalian counterparts of ___ and ___.

A

Dice; RISC

65
Q

RNAi for studying mammalian genes

Two ___ at the 3’ overhang makes it more stable.

A

Uracils

66
Q

RNAi for studying mammalian genes

___ group can be added to 2’-OH ribose.

A

Methyl

67
Q

RNAi for studying mammalian genes

Purified dicer can also be used to produce ___.

A

siRNA

68
Q

RNAi for studying mammalian genes

___ can be designed to express different shRNA molecules.

A

Vectors

69
Q

RNAi for studying mammalian genes

Two complementary sequences about 20 nucleotides in length separated by a __ __.

A

Loop region

70
Q

RNAi for studying mammalian genes

When the vector is transformed into a cell, the shRNA is transcribed and activates ___ ___.

A

Gene silencing

71
Q

___ ___ are designed to express dsRNA for each gene in the genome.

A

RNAi libraries

72
Q

RNAi libraries are used to..

A

Identify the role of unknown proteins

73
Q

Mammalian cells can be screened for defects induced by an RNAi library clone using a ____ or ___.

A

Live cell microarray

Multi-plate assay

74
Q

Eukaryotic mRNA splicing

Researchers had expected the complementary of upstream (5’) and downstream (3’).

However, this idea was soon ___.

A

Discounted

75
Q

Eukaryotic mRNA splicing

The sequences at 5’ and 3’ are not ___, yet not ___.

A

Complementary; random

76
Q

Eukaryotic mRNA splicing

Almost all introns begin with ___ and end with ___.

A

G:U

A:G

77
Q

Eukaryotic mRNA splicing

The branch site -

A

Sequences with introns, 20-50 nucleotides just upstream of 3’, is essential for splicing

78
Q

Eukaryotic mRNA splicing

Splicing is carried out by a complex of proteins and RNA called the __.

A

Spliceosome

79
Q

Alternative mRNA splicing

A
  • often produces two forms of the same protein that are necessary at different stages of development or in different types of cells
80
Q

___ of the lgM class exist either a membrane bound protein displayed on the cell surface or as a soluble protein secreted into the blood.

A

Immunoglobulins

81
Q

___ are mRNA sequences that bind directly to effector molecules to control the expression of the mRNA into protein by attenuation or translational inhibition mechanisms.

A

Riboswitches

82
Q

__ __ __ occurs during growth conditions.

A

Cell wall synthesis

83
Q

Cell wall synthesis

A

When the cell is growing, levels of UDP-GIcNAc are low and quickly incorporated into cell wall

If the cell is not growing, the excess UDP-GIcNAc binds to a riboswitch on the glms gene

Activates the self-cleaving ribozyme to degrade mRNA

84
Q

Small naturally occurring ribozymes

A

Found in small subviral agents such as viroids and satellite viruses

They have common motifs that catalyze RNA cleavage

85
Q

Engineering ribozyme for applications

A

Adding a ribozyme motif such as the hammerhead or hairpin region from the small ribozymes can make antisense oligonucleotides more stable because they are not degraded.

These constructs cut the target mRNA without the use of Rnase H

86
Q

In vitro selection of ribozymes

A

Can also generate new ribozymes by mixing random sequences that represent potential ribozymes with a specific substrate

87
Q

In vitro evolution of ribozymes

A

Adding a mutagenesis step to the in vitro selection procedure allows the ribozyme to “evolve” into a better enzyme

88
Q

Combining riboswitches and ribozymes

A

Ribozymes that only act in presence of effector molecules

89
Q

Antisense

A

RNAnase H

90
Q

RNAi

A

RISC

91
Q

Ribozyme

A

Cuts by itself

Biotechnology I (14 decks)

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