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BIOL 200 - Molecular Biology > Lecture 24 - RNA Processing II > Flashcards

Lecture 24 - RNA Processing II Flashcards

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1
Q

What structure is RNA processing linked to?

A

CTD of RNA pol II

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2
Q

Why does RNA pol II pause after 25 nucleotides?

A

It pauses because it is associated with negative regulators of elongation that hang on to polymerase and impede its progress and force it to slow down and eventually stop.

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3
Q

What mediates the phosphorylation of ser5?

A

Protein Kinase TFIIH

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4
Q

Why does the 5’ end of elongating mRNA need to be modified?

A

It needs to be modified because if it is exposed, the RNA will get degraded by exonucleases as it is made.

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5
Q

What recruits the capping enzyme during transcription?

A

CTD Ser5 Phosphorylation

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6
Q

What type of bond joins the 5’ cap to an mRNA?

A

5’-5’ Triphosphate Linkage

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7
Q

What is the 5’ cap made out of?

A

7 Methylguanylates

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8
Q

When is ser2 phosphorylated?

A

Ser2 is phosphorylated after CDK9/cyclin-T joins the complex (after capping).

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9
Q

What releases the negative regulations of elongation?

A

Ser2 Phosphorylation

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10
Q

What happens to the branch point A when U2 snRNA interacts with the intron RNA around it?

A

The adenosine bulges out, making it available to interact during the splicing reaction.

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11
Q

What happens if you add in oligonucleotides around a splicing reaction?

A

They block the interaction between the RNAs (mRNA and snRNA) and therefore stop splicing.

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12
Q

What is special about a debranching enzyme that makes it necessary to have over a normal exonuclease?

A

The debranching enzyme will cleave the 2’-5’ linkage in the lariat structure, which is atypical in cells can’t be cleaved by exonucleases.

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13
Q

What was found in the 80s in tetrahymena (a protist)?

A

It was found that at least one splicing reaction (that also takes place in human RNA) could occur without any protein whatsoever.

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14
Q

What must be necessary for self-splicing introns to function?

A

Magnesium

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15
Q

In what process do RNA act as the substrates, products, and enzymes that carry out the activity?

A

Self-Splicing

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16
Q

What type of splicing occurs in group 1 organisms?

A

Group 1 organisms, like tetrahymena, exhibit self-splicing. They can be distinguished because they use guanosine as their branch point instead of adenosine.

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17
Q

What type of splicing occurs in group 3 organisms?

A

Group 3 organisms exhibit splecosome mediated splicing. They need U1 snRNA, U2 snRNA, and other snRNPs to come together to perform the 2 trans-esterification reactions and splice out the lariats.

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18
Q

What type of splicing occurs in group 2 organisms?

A

Group 2 exhibit self-splicing that is more similar to spliceosome splicing that occurs in group 3 than the self-splicing that occurs in group 1. They rely on the 2’-5’ interaction with branch point A to splice out the intron.

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19
Q

Where does group 2 splicing occur?

A

Mitochondria and Chloroplasts

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20
Q

How do group 2 introns splice?

A

Group 2 introns fold up into a very complex secondary structure consisting of stem loops that bring together the sites where splicing will take place.

21
Q

Which splicing group has the most diverse introns: 2 or 3? Why?

A

Group 3 has more diverse introns because the sequence of group 2 introns is more limited so that the necessary structure for self-splicing can occur.

22
Q

What is used to help cells determine where to splice?

A

U2AF

23
Q

What do the two subunits of U2AF do?

A

The first subunit will bind to the region aroudn the AG at the 3’ terminus of the intron to be splice out. The other subunit will interact with the first subunit and will also interact with the polypyrimidine tract (pyrimidine rich region) which is relatively close to the branch point A.

24
Q

What does U2AF use to determine which AG di-nucleotide to bind to?

A

SR Proteins

25
Q

Where can SR proteins be found?

A

SR proteins can be found decorating exons.

26
Q

What do SR proteins have an affinity for?

A

Exonic Splicing Enhancer (which are inherent in the exon sequences)

27
Q

Which type of protein contain RRM (RNA binding) domains and critical for distinguishing borders of exons so that the spliceosome machinery knows where to splice?

A

SR Proteins

28
Q

What does the cross-exon recognition complex consist of?

A

It consists of the SR proteins, exonic splicing enhancers, and other proteins that play a role in defining the exonic boundaries and determining the appropriate splicing regions.

29
Q

What is AAUAAA a signal for?

A

Polyadenylation

30
Q

What was always found near the terminated regions or in upstream regions before the poly A tail in cDNA?

A

AAUAAA followed by a U or G/U rich region was always found.

31
Q

What happens if the AAUAAA sequence in pre-mRNA is mutated?

A

The mRNA is quickly degraded or very unstable.

32
Q

What happens when RNA pol II comes across the polyadenylation signal?

A

CPSF (cleavage and polyadenylation specificity factor) comes in and recognizes the AAUAAA sequence. Other proteins follow and interact more specifically with the G/U region further in the 3’ direction. Then PAP (poly A polymerase) joins the complex, the 3’ end of the pre-mRNA is cleaved, and A residues are attached (via PAP) to where the 3’ end was cleaved.

33
Q

What would happen if a pre-mRNA were cleaved before PAP joins the complex?

A

The 3’ end would be vulnerable to exonucleases that could degrade it.

34
Q

What are the two phases of polyadenylation mediated by PAP? What happens during each of them?

A

Slow Phase: PAP adds on a few adenosines (about 12). It works slow because it doesn’t work well without poly A binding protein N1 (PABPN1).

Rapid Phase: PABPN1 binds to this structure and enhances PAP’s activity so that it can add on about 200 adenosine residues.

35
Q

Which type of mRNA is not polyadenylated? What happens instead to ensure these mRNAs are not degraded?

A

Histone mRNAs are not polyadenylated. Instead, they have a special secondary structure in their 3’ UTRs that is important for allowing them to evade degradation from 3’-5’ exonucleases.

36
Q

How much of the cell’s RNA is rRNA?

A

70-80%

37
Q

From which region of the DNA are rRNAs transcribed?

A

rDNA

38
Q

If you take the regions that correspond to the rDNA and put them into the nucleus or separate them from the rest of the DNA, what happens?

A

The nucleolus will be formed (via rRNA transcription).

39
Q

What is the site or rRNA transcription?

A

Nucleolus

40
Q

What sets the nucleolus apart from other organelles?

A

The nucleolus is not a membrane-bound organelle. Rather, it is an example of liquid-liquid phase separation. The nucleolus is phase separated from the rest of the nucleoplasm.

41
Q

What can be said about rRNA transcription in different organism?

A

In general, all organisms that make rRNA do so by transcribing the same highly conserved sequence. It is transcribed in the same manner in every organism that has been examined.

42
Q

What exists between exons in rRNA molecules being transcribed in humans?

A

Transcribed Spacers

43
Q

What type of molecules mediates post-transcriptional modification of rRNA?

A

snoRNAs (small nucleolar RNAs)

44
Q

What do snoRNAs form when they interact with proteins?

A

snoRNPs

45
Q

What leads to uridine residues being modified into pseudouridine?

A

SnoRNAs base pair with stem loops in order to specify this modification.

46
Q

What transcribed pre-tRNAs?

A

RNA pol III

47
Q

What modification are made to pre-tRNA to convert it to tRNA?

A

The 5’ end is removed, some nucleotides in the sequence are modified (uridine into psuedouridine), a di-nucleotide is removed and replaced by a CAA sequence 3’ end, and in some cases, (like in tyrosine), a big piece of the RNA is spliced out.

48
Q

How does mRNA and tRNA splicing differ?

A

tRNA splicing does not result in the formation of lariats like in mRNA splicing. Rather, two cuts are made, the necessary piece is removed, and the the tRNA is rejoined.

BIOL 200 - Molecular Biology (22 decks)

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