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MAMS BCH Exam III > Offner RNA > Flashcards

Offner RNA Flashcards

1
Q

Difference in RNA processing for eukaryotes vs prokaryotes

A

Prokaryotes have no compartments for processing, eukaryotes do

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2
Q

What % of RNA is tRNA, rRNA and mRNA

A

95% tRNA, rRNA
1-5% mRNA

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3
Q

The template strand is the coding or non-coding strand

A

Non-coding

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4
Q

Structure of prokaryotic RNA Pol

A
  • beta subunit
  • sigma subunit
  • core enzyme: alpha2, beta, beta’

Prokaryotes

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5
Q

Structure of RNA Pol holoenzyme

A

alpha2, beta, beta’, sigma

Prokaryotes

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6
Q

Beta subunit of prokaryotic RNA Pol

A

Contains catalytic site
- synthesizes 3’-5’ phosphodiester bonds

Prokaryotes

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7
Q

Sigma subunit of prokaryotic RNA Pol

A

Recognizes promoter regions
- initiates transcription
- binds -10, -35

Prokaryotes

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8
Q

Does bacterial transcription require a primer?

A

Nahh bb

Prokaryotes

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9
Q

Where is the prokaryotic promoter region written, and what two sequences does it consist of?

A

On the sense strand
- non-transcribed strand
- coding strand
consists of -35 and -10

Prokaryotes

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10
Q

-35 region sequence

A

TTGACA

Prokaryotes

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11
Q

Pribnow sequence (-10)

A

TATAAT

Prokaryotes

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12
Q

What is the importance of the distance between the Pribnow and -35 region

A

Allows for the efficient intiation of transcription

Prokaryotes

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13
Q

How does prokaryotic transcription start

A

The core binds to random promoter and non-promoter regions
- sigma binds core, if bound to non-promoter, RNA Pol released
- holoenzyme opens DNA 12bp

Prokaryotes

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14
Q

2 different NT binding sites of beta subunit of RNA Pol

A

1st for Purine
- creates different phosphodiester bond
2nd for all subsequent dNTPs

Prokaryotes

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15
Q

Rho-independent termination

A

RNA Pol slows down in GC-rich palindrome region
- Hairpin forms, NRA released due to weak following A/U bonds
- must end with UUUUU region

Prokaryotes

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16
Q

Rho-dependent termination

A

Rho contains helices, ATPase
- Rho waits for RNA Pol to slow down
- Rho moves to 3’ end of RNA by hydrolyzing ATP
- unwinds DNA/RNA to release RNA

Prokaryotes

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17
Q

Actinomycin D

A

Initiation and elongation inhibitor
- intercalates in major groove to prevent unwinding
- effective in both prok and euk
- also doxorubicin

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18
Q

3 eukaryotic polymerases

A

1) RNA Pol I
2) RNA Pol II
3) RNA Pol III

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19
Q

Which RNA Pol transcribes tRNAs?

A

RNA Pol III

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20
Q

Which RNA Pol transcribes mRNAs?

A

RNA Pol II

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21
Q

Which RNA Pol transcribes miRNAs, snRNAs?

A

RNA Pol II

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22
Q

Which RNA Pol transcribes the rRNA for the 4 subunits?

A

RNA Pol I: 28s, 18s, 5.8s
RNA Pol III: 5s

23
Q

Where are RNA Pol 1,2,3 located?

A

RNA Pol I in nucleolus
RNA Pol II and III in nucleus

24
Q

Which RNA Pol transcribes small RNAs

A

RNA Pol III

25
Q

RNA Pol II structure

A

12 subunits
- core promoter binds to 3 regions

26
Q

3 regions core promoter binds to

A

Basal (site of transcription initiation) , Constitutive (rate), Inducible (response to environmental elements)

27
Q

Where is the enhancer region located

A

Anywhere upstream of the core promoter

28
Q

Does formation of the basal transcription complex require ATP?

A

Yes, requires ATP hydrolysis

29
Q

Components of the basal transcription complex

A

TBP
TAF
TFII (A,B,F,E,H)

30
Q

TBP

A

TATA box binding protein

31
Q

TAF

A

TATA associated factors

32
Q

TFII

A

Transcription factors for Pol II

33
Q

Which kinase phosphorylates Pol II

A

TFII H

34
Q

How does eukaryotic transcription elongation start?

A

TFIIF and Pol II detach from the basal transcription complex

35
Q

What occurs during termination

A

Dephosphorylation of Pol II and TFII F complex

36
Q

Initiation of RNA Pol I

A

UBF and CBF combine to causes a conformational change in the DNA which allows RNA Pol I to bind and initiate transcription

UBF = Upstream Binding Factor
CBF = Core Binding Factor

37
Q

Initiation of RNA Pol III

A

Starts on internal promoter (within the gene)
- TFIII B binds upstream, C and A bind by the +1
- Pol III binds, TFIIII C/A release, transcription initiated

38
Q

Amanita Phalloides contains alpha-amanitin. Why is it dangerous?

A

Present in eukaryotes only
- Fully inhibits RNA Pol II, and inhibits RNA Pol III a little
- no mRNA, no proteins, liver failure, death!

39
Q

What is hnRNA

A

mRNA without any modifications

40
Q

Where do mRNA modifications take place

A

Nucleus, required for exit into the cytoplasm

41
Q

mRNA 5’ cap

A

Backwards GTP added to 5’ end
- 5’5’ tri-P linkage
- 2 from mRNA attach to one on GTP

42
Q

Guanylyl Transferase

A

Removes gamma P from RNA and PPi from reversed GTP to add 5’ cap to mRNA

43
Q

3’ polyA tail

A

specific endonuclease cleaves 11-30 NTs downstream of AAUAAA signal region
- PolyA polymerase hydrolyzes ATP and adds 200 A residues to mRNA

44
Q

Splicing mechanism

A

1) U1 RNA base pairs with 5’ splice junction
2) U2 binds branch site
3) U4/5/6 bind to bring intron 1 splice site near branch point
4) U1/4 leave, U6 binds to U2
5) 2’ OH of A attacks 5’ splice site
6) 3’ OH of exon 1 attacks 3’ splice site
7) exons are joined, intron leaves

45
Q

Why does splicing occur

A

Different sets of RNA binding proteins in different tissues

46
Q

How does Thalassemia occur

A

A new 3’ splice site results from point mutation
- stop codon brought forward
- truncated protein

47
Q

How is tRNA produced in prokaryotes

A

As multimers
- cleaved by RNAses at 5’ and 3’ ends
- bases get modified
- CCA added to 3’ end by tRNA nucleotidyl transferase

48
Q

How is tRNA produced in eukaryotes

A

Monomeric
- contains intron to prevent premature mRNA binding
- removed by endonuclease and ATP-dependent ligation

49
Q

How do the ribosomal subunits assemble

A

Self-assemble

50
Q

Mechanism by which eukaryotic ribosomes are formed

A

Precursor is spliced to 45S, which self-splices to 28S, 18S, and 5.8S
- 28S, 5.8S and 5S combine to make large subunit (60s)
- 18S becomes 40S
- small and large subunits enter cytoplasm separately
- 5S comes from RNA Pol III

Small and large subunits only combine if they are actively transcribing

51
Q

Prokaryotic ribosome combos

A

25 + 5 = 50
16 = 30
Total = 70S

52
Q

Eukaryotic ribosome combos

A

28:5.8 + 5S = 60
18 = 40
Total = 80S

53
Q

Structure of rRNA precursor

A

one of each subunit rRNA

54
Q

Where do all the eukaryotic rRNA precursors combine to make the large and small subunits?

A

Nucleolus

MAMS BCH Exam III (12 decks)

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