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Bioc2003 > RNA > Flashcards

RNA Flashcards

1
Q

What are some key features of RNA polymerase?

A 
Synthesises in 5'-3' direction
Prokaryotes have 1, eukaryotes have 5
Does not require primer
RNA product does not remain base paired to template
Shape of crab claw
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2
Q

Which strand is antisense?

A

Template strand

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3
Q

What is the core polymerase?

A

a2bb’omega

  • alpha: scaffolding role
  • beta: polymerase active site
  • beta’: DNA binding
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4
Q

What is the main type of sigma factor?

A

sigma70

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5
Q

What is the role of the sigma factor?

A

Transcription initiation/promoter recognition

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6
Q

What is Rho factor?

A

6 ringed protein
Binds RNA at termination recognition sequences, rut sites
Binds ss RNA
Doesn’t bind RNA being translated
Rho pulls RNA out of polymerase, induces polymerase conformational shape such that polymerase terminates

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7
Q

What is Rho-independent termination? (intrinsic)

A

Rho protein isn’t used.

A hairpin loop forms due to inverted repeats in DNA to signal end of transcription.

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8
Q

What is Rho-dependent termination?

A

Rho travels along RNA transcript unti it reaches RNA pol, causes dissociation from RNA (or dna).

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9
Q

What is the prokaryote transcription unit?

A

polycistronic mRNA -

- which encodes two or more proteins

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10
Q

How is prokaryotic tRNA processed?

A

endonucleases eg RNAse P cleave primary transcript
RNase D trims/digests 3’ end
tRNA nucleotidyl transferase adds CCA to end (2CTP + ATP –> 3PPi + CCA)

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11
Q

What is the function of RNA pol I?

A

Transcribe ribosomal RNA (45S precursor of 28S, 18S and 5.8S rRNA)

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12
Q

What is the function of RNA pol II?

A

Transcribe protein-coding genes, sn RNAs, U1, U2

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13
Q

What is the function of RNA pol III?

A

Transcribe tRNA, 5S rRNA, Alu repeated sequences

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14
Q

How is euk pre-rRNA processed?

A

Primary transcript is cut to yield mature rRNAs in ribosomes.

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15
Q

Which RNA pol is insensitive to alpha amanitin?

A

RNA Polymerase I

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16
Q

Which RNA pol is very sensitive to alpha amanitin?

A

RNA polymerase II

17
Q

What is the eukaryote equivalent of operon?

A

Transcription units of rRNA

18
Q

What is the preinitiation complex in TATA box dependent core promoters?

A

purified factors can assemble into a transcription preinitiation complex (PIC) in the following order: TFIID, TFIIB, RNA polymerase II-TFIIF complex, TFIIE, and then TFIIH

19
Q

What are some regulatory sequence elements of RNA polymerase II core promoter?

A

BRE (TFIIB recognition element), TATA, Inr, DPE (downstream promoter element)

20
Q

What are the steps of mRNA processing in eukaryotes?

A

1) transcription, 5’ capping
2) cleavage at polyA site
3) polyadenylation
4) RNA splicing

21
Q

Which transcription factor binds TATA box?

A

TFIID
TBP is part of this
TFIID then recruits TFIIA and TFIIB

22
Q

What is the order of transcription factors binding RNA before RNA polymerase is in position?

A 
TFIID binds TATA box
TFIIA and TFIIB are recruited
TFIIF is recruited
Polymerase is brought into position (bound with tfiif)
TFIIE assists TFIIH (helicase activity)
23
Q

What is triggered by formation of PIC?

A

Phosphorylation of polymerase C-terminal domain CTD and melting of DNA (by helicase TFIIH) to form transcription bubble
Transcription can start with ss DNA

24
Q

Which transcription factor has kinase activity?

A

TFIIH - phosphorylates residues on polymerase tail so enzyme can escape promoter, continue to transcribe downstream

25
Q

What is the structure of 5’ methylated cap?

A

7 methylated guanine of euk mRNA
5’-5’ linkage
methyl group on 2’ OH of 1st mRNA nucleotide

26
Q

What is RNA splicing?

A

Removing introns, putting exons together for RNA sequence to translated into gene product
Same DNA sequence can be used for multiple products

27
Q

What is the splicing reaction?

A

2 trans-esterification reactions
adenine in branch site breaks phosphodiester bond
nuclephilic attack on splice site

28
Q

What is the spliceosome?

A

Machine size of ribosome
Comprises 150 proteins, 5 sn RNAs (U1, U2, U4, U5, U6)
Each RNA complexed with several proteins
Hydrolyses ATP

29
Q

What is a snrnp?

A

small nuclear ribonucleo proteins, are RNA-protein complexes that combine with unmodified pre-mRNA and various other proteins to form a spliceosome, a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs.

30
Q

What are CpG islands?

A 
Often housekeeping genes
Increase CpG in 5' region of genes
long stretches eg 1-2kb
29k CpG islands in human genome
Some found in tissue specific genes
(Unmethylated when actively transcribed)

Bioc2003 (5 decks)

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