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EOM 1 - Test 2 > Primerano - Transcription and RNA Processing (I/II) > Flashcards

Primerano - Transcription and RNA Processing (I/II) Flashcards

1
Q

What is the role of Ribosomal RNA (rRNA)?

A

WIth ribosomal proteins, make up the ribosome organelle that translate the mRNA

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2
Q

Transfer RNA (tRNA)

A

Shuttles Amino Acids to ribosomes during translation

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3
Q

Messenger RNA (mRNA)

A

Encodes amino acid sequence of a polypeptide (RNA polymerase makes from ssDNA to leave the nucleus towards the ribosome for transcription)

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4
Q

Small Nuclear RNA (snRNA)

A

With proteins, forms complexes that are used in RNA processing in eukaryotes

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5
Q

What is the role and impact of non-standard bases in RNA?

A

~ 10% of all bases in tRNA modified, these change base pairing properties and stabilize hairpin loops

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6
Q

What are the main two differences between transcription in prokaryotes and eukaryotes?

A

In eukaryotes transcription is temporally and spatially separated

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7
Q

What is the difference between housekeeping and tissue specific genes?

A

Housekeeping are uniform throughout an organism, tissue specific are localized to micro environments for a specific purpose–e.g. RBCs have Hb, other’s don’t

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8
Q

What is a major requirement in eukaryotic transcriptional initiation?

A

GTFs (General Transcription Factors)

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9
Q

What is the major role of TFII-H?

A

Helicase and kinase activity

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10
Q

What leads to dissociation of Pol-II from the preinitiation complex?

What does this signal the start of?

A

Phosphorylation of 5th serine residue by TF2-H

Initiation of transcription

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11
Q

What does RNA Pol I transcribe?

What processes it?

A

Single gene, precursor of large ribosomal rRNA (18S, 28S, +5.8S)

Cleaved by Rnases

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12
Q

What does RNA Pol II transcribe?

What is unique about RNA Pol II?

A

All mRNA genes, as well as microRNA precursors and most snRNA involved in splicing.

Only Pol II transcripts are poly-adenylated

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13
Q

What does RNA Pol III transcribe?

What recruits Pol III?

A

Small genes like tRNA, U6 snRNA, and 5S rRNA gene

Transcription Factors bind downstream to recruit Pol III (each listed above has different TFIII’s)

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14
Q

What is a eukaryotic promoter?

Where is it located?

What do they contain?

A

Regulatory region of DNA providing control point for regulated gene transcription

Located upstream (toward 5’ region)

Contain transcription factors

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15
Q

What is the difference between prokaryotic and eukaryotic promoters?

A

Prokaryotes: Two short sequences -10, -35 (upstream); -10 = Pribnow Box (TATAAT; -35 = TTGACA

Eukaryotes: Diverse, usually upstream and more regulated, many contain TATA Box

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16
Q

How is pre-rRNA processed in eukaryotes? Where does this occur?

A

Pre-rRNA is processed via cleavages, processing occurs in the nucleolus, which acts as a ribosomal factory

17
Q

What molecules participate in cleavage and are capable of hydrogen bonding with pre-rRNA?

A

Small Nucleolar RNA (snoRNA) and Small Nucleolar Ribonucleoparticles (snoRNPs)

18
Q

What is tRNA originally transcribed as?

What process occurs at the 3’ end?

A

pre-tRNA

RNAse P (RNA-protein complex) cleaves the 3’ end, and CCA end is added (site of AA attachment)

19
Q

What are methods of regulation for RNA reactions?

A

Hydrogen Bonding, Methylation, and Chemical Conversion of Bases (e.g. uridine to pseudouridine)

20
Q

Describe the process of capping.

What is unique about this linkage?

What role does the cap play?

A

Addition of 7-methyl guanidine to 5’ end

Rare 5’-5’ phosphodiester linkage–stabilizing factor due to long half life

Stabilize mRNA, helps align with ribosome

21
Q

Describe the process of tailing.

An area rich in what bond pairs is downstream to the site?

What is the role of the Endonuclease?

What does capping attract?

A

Adds 10-30 bases upstream at the AAUAAA signal

G-U rich element is downstream

Cleaves the chain and poly-A-polymerase adds a poly-A tail of ~ 200 bases

Poly-A tail attracted to phosphorylated CTD of RNA Polymerase

22
Q

What is the first step in splicing?

What does this leave?

What is joined following this?

What is formed?

A

Cleavage of 5’ splice site, leaves exon with free 3’ end

The 5’ end is joined with the 2’ hydroxyl of adenine that is near the 3’ end of the intron–forming the lariat

23
Q

What is the second step of splicing?

Once this occurs, what happens next?

A

Cleavage of the 3’ site releases the lariat

The 3’ exon is joined with the 5’ exon

24
Q

Where does splicing take place?

What are their subunits?

A

Spliceosomes

5 types of snRNA to form snRNPs

25
Q

What causes the bending of the lariate in splicing?

A

U1 binding with U2

26
Q

When is the first exon cleaved and the lariat formed?

A

When U6 forms complex with U2

27
Q

What leads to the cleavage and removal of the lariate intron and linking the first and second exons?

A

U5 binding the 3’ site

28
Q

What receuits snRNPs to initiate spliceosome assemble?

What recruits U2 to the 3’ site?

A

SR proteins

U2AF

29
Q

What exists to vary order of inclusion of exons/introns w/in RNA message?

How is this accomplished?

Is there additional regulation?

A

Alternative Splicing

Activators brining snRNPs to alternative sites

Some factors may act a repressors

30
Q

What is the majority of mRNA? What does this result it?

How are these targeted?

A

Over 90% pre-mRNA = introns, which need to be degraded

Lariats are targeted by enzymes recognizing the unique 2’-5’ phosphodiester bond

Enzymes also target naked 3’ and 5’ ends (not capped)

31
Q

What may trigger nonsense mediated mRNA decay?

A

Premature termination codons

32
Q

How is decay rate related to controlling expression?

How does the poly-A tail factor in?

What can further stabilize/destabilize mRNA?

A

Shorter half-lives = regulatory proteins (rapid response)

Longer half-lives = structural proteins

Length of poly-A tail related to half-life

Factors can bind 3’ end to stabilize, or the 5’ end to block translation

EOM 1 - Test 2 (18 decks)

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