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Molecules to Medicine Unit 1 > RNA > Flashcards

RNA Flashcards

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Organic Chemistry 101 flashcards
1
Q

How is RNA hydrolyzed?

A

RNA is far more easily hydrolyzed than DNA due to nucelophilic attach by 2’ OH on the phosphodiester bond.

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2
Q

What are the three classes of RNA in the human cell?

A

Structural RNA, Regulatory RNA and Information-Containing RNA

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3
Q

How does puromycin mimic amino-acyl tRNA to terminate translation?

A

Puromycine is a nucleotide analog that mimics the tRNA acceptor region, targeting the acceptor stem loop, and binding to the ribosome as it elongates the polypeptide chain to terminate translation.

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4
Q

Transcription Unit

A

The segment of DNA which gets transcribed into RNA

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5
Q

Gene

A

Transcription unit flanked non-transcribed “regulatory” DNA seqeunces

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6
Q

The first base pair where transcription initiates is designated __________

A

+1

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7
Q

Downstream, bases are assigned ________ numbers

A

Positive

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8
Q

Upstream, bases are assigned ___________ numbers

A

Negative

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9
Q

RNA pol II makes ___________

A

mRNA

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10
Q

RNA transcript is read from the __________ and mimics the ___________

A

DNA template strand; DNA nontemplate (coding) strand

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11
Q

Enhancers

A

Enhance promoters; can be upstream or downstream; can also be an intron

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12
Q

Transcription always begins on ___________

A

Exon 1

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13
Q

DNA binding domain

A

Segment in a protein which recognizes the correct DNA sequence (promotor)

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14
Q

Activation domain

A

Facilitates protein-protein contact with general transcription factors

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15
Q

RNA synthesis is __________ and ___________, meaning it can only grow from one end.

A

Unidirectional; processive

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16
Q

Explain the five steps in the transcription cycle common to bacterial and eukaryotic polymerases.

A
  1. RNA polymerase sits on the promoter sequence, upstream of the transcription start site
  2. The double-stranded DNA is opened, creating a transcription bubble and exposing the template strand
  3. RNA nuceloside triphosphates come and lay themselves down after polymerase creates the phosphodiester linkage of two initial rNTP’s
  4. Reaches the end of a gene and gets signal to terminate transcription
  5. RNA polymerase lets go of template (DNA) and RNA product
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17
Q

Promoter escape

A

Point where RNA polymerase begins moving

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18
Q

When is the moment of initiation?

A

When the polymerase catalyzes the phosphodiester linkage of two initial rNTP’s

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19
Q

When does regulation of transcription occur?

A

Regulation of transcription occurs during initiation and elongation

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20
Q

Function of RNA polymerase I

A

Make rRNA

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21
Q

Where are polymerase I-III located?

A

Nucleus

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22
Q

Polymerase I-III are in the same family as _________

A

bacterial RNA polymerase

23
Q

Function of polymerase II

A

Makes mRNA, snRNA, miRNA, incRNA

24
Q

Where is polymerase IV located?

A

In the mitochondria

25
Q

What is a promoter?

A

Promoters direct RNA polymerase to the start of genes; control the direction and frequency of transcription

26
Q

Binding of the ________ to the_______ helps direct assembly of the pre-initiation complex at the promoter.

A

TATA box binding protein; TATA box

27
Q

Where is the TATA box located?

A

In the minor groove

28
Q

What is the promoter recognition factor in RNA polymerase II?

A

TFIID

29
Q

Alpha-AMantin, from the death cap mushroom Amnita phalloides is a ___________ inhibitor of RNA pol II. It binds to the _______ and blocks RNA chain elongation by preventing translocation.

A

non-competative inhibitor; bridge helix

30
Q

Rifampin is an __________ which binds to bacterial RNA polymerase and blocks the ________

A

Antibiotic, RNA exit channel

31
Q

What is TFIID transcription factor’s role in the pre-initiation complex

A

Recognizes the TATA box

32
Q

What is TFIIB transcription factor’s role in the pre-initiation complex?

A

Positions RNA polymerase at the start site of transcription.

33
Q

What is TFIIF transcription factor’s role in the pre-initiation complex?

A

Stabilizes RNA polymerase interaction and attracts TFIIE and TFIIH

34
Q

What is TFIIH transcription factor’s role in the pre-initiation complex?

A

Unwinds DNA at transcription start point, phosphorylates Ser3 of the RNA polymerase CTD, releases RNA polymerase from the promotor

35
Q

TFIIH is a _________ and a ___________

A

Transcription factor; DNA repair factor

36
Q

What is the function of XPB helicase of the TFIIH transcription factor?

A

XPB helicase opens DNA at the promoter to permit initiation of transcription

37
Q

What are the three diseases associated with TFIIH mutation?

A

Xeroderma pigmentosum, Cockaynes syndrome and trichothiodystrophy

38
Q

What the three benefits in the addition of the Poly-A tail?

A
  1. Binds to the poly A binding protein 2. Protection from degradation on the 3’ end 3. Enhanced translation
39
Q

What the three major ways in which most pre-RNA’s are processed?

A
  1. Capping 2. Splicing 3. Cleavage/polyadenylation
40
Q

During capping of the _________ end, the first base is replaced by a cap, Which is a _________ structure that is added backwards.

A

5’; Guanine

41
Q

What are the three main function of the 5’ cap of the mRNA?

A
  1. Protects the 5’ end from exonucleases 1. Provides a recognition site 3. Decapping is the initiation of degradation of mRNA
42
Q

What is elF4E?

A

elF4E is a cap-binding protein and a critical stimulator of translation on ribosomes

43
Q

What are the three enzymatic reactions required to add a 5’ cap to pre-mRNA?

A
  1. Triphosphatase removes a phosphate 2. Guanyltransferase adds a GMP backwards 3. Guanine 7 methyl transferase methylates the N7 position on Guanine
44
Q

What is the sequence at the 5’ splice site?

A

GU/GT

45
Q

What is conserved within every branch point?

A

‘A’ residue

46
Q

What is the sequence at the 3’ splice site?

A

AG

47
Q

What is the consensus sequence at the poly-A tail?

A

AATAA/ AAUAA

48
Q

What is the Spliceosome?

A

Ribonucleoprotein complex composed of multiple small nuclear ribonuceloprotins (snRNPs)

49
Q

What is Marfan’s Syndrome?

A

A dominant autosomal disease caused by a mutation that disrupts splicing of the fibrullin gene transcript (connective tissue)

50
Q

What is the function of U1 snRNA?

A

The 5’ splice site is recognized by base-pairing to the U1 snRNA

51
Q

What is the function of U2 snRNA?

A

The branch point is recognized by base pairing to the U2 snRNA

52
Q

What are the two reaction that make the mature 3’end of RNA?

A
  1. Cleavage 2. Polyadenlyation
53
Q

________ fails to _________ without the Poly A tail.

A

RNA polymerase; terminate

Molecules to Medicine Unit 1 (10 decks)

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