CHEM 441A+B > Chapter 21: Transcription > Flashcards

Chapter 21: Transcription Flashcards

(38 cards)

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1
Q

What is transcription?

A

DNA dependent synthesis of RNA

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2
Q

What is mRNA, tRNA, and rRNA?

A

mRNA: Encodes amino acid sequence of proteins (instructions)

tRNA: Reads info in the mRNA (adapter)

rRNA: Consitutes ribosome, makes proteins (machinery)

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3
Q

What are the functions of other RNAs?

A

Regulatory or catalytic function

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4
Q

Which strand is used to synthesize the mRNA strand?

A

The antisense strand (complimentary). The mRNA is identical to the sense strand. Thymine gets replaced with uracil in RNA.

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5
Q

What are the three steps in transcription?

A

Initiation, Elongation, Termination

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6
Q

Compare and contrast Transcription and replication?

A

Transcription:
- No primer needed
- Involves limited segments of DNA
- Only one DNA strand serves as the template

Replication
- Requires primer
- Involves entire strand of DNA
- Requires both strands of DNA

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7
Q

What does RNA polymerase do?

A
  • Search for initiation (promoter)sites
  • Unwind DNA to produce single strand DNA template
  • Catalyze formation of a phosphodiester bond
  • Detect terminal signals
  • Interact with activator and repressor proteins that regulate transcription
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8
Q

How is proofreading in Transcription different from DNA replication?

A
  • Higher error rate (1 in 10^4 to 10^5 ribonucleotides)
  • Lack 3’ ->5’ proofreading exonuclease activity
    • RNA Pol corrects errors by removing mismatch from 3’ end by reversing Pol reaction
  • Lower RNA synthesis fidelity can be tolderated because it is not transmitted to progeny (except viruses)
  • RNA eventually is degraded and replaced
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9
Q

What do the subunits of RNA Pol in E.coli do?

A
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10
Q

What does the sigma(σ) factor do?

A

Interacts with the core of RNA Pol to recognize the -35 and -10 boxes

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11
Q

What is a promoter?

A
  • A sequence where RNA Pol can bind around boxes -35 and -10 which are important for σ70 subunit
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12
Q

How is the strength of a promoter sequence determined and what does that mean for the transcription rate?

A
  • If a gene has a strong promoter which will match the consensus sequence
    • Will be transcribed frequently (every two seconds)
  • If a gene has a weak promoter it wont match the consensus sequence well
    • Will be transcribed less frequently (every 10 minutes)
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13
Q

Draw the transcript bubble and include the channels and labeled ends.

A
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14
Q

Outline the steps of prokaryotic transcription.

A
  • RNA Pol binds to promoter at -35 and -10
  • DNA is partially unwound
  • RNA synthesis initiated in a primer-independent reaction
  • Sigma factor is released
  • elongation continues (28-80 bases/s)
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15
Q

Describe the termination of Transcription.

A
  • Termination signaled by specific sequences
  • If RNA Pol is released prematurely it must start over again
  • E.coli has two termination signals
    • Rho dependent (Rho is a protein factor)
    • Rho independent
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16
Q

Describe Rho-dependent termination.

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A
  • Caused by Rho binding to C rich region
  • Rho is a helicase that destabilizes the RNA:DNA helix thus terminates transcription
17
Q

Describe Rho-independent termination.

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A
  • Intrinsic termination
  • Depends on presence of certain sequence
  • Termination sequence on the template consist of GC rich followed by AT rich region
  • Forms stem loop at GC rich region
  • Stem loop causes Pol to pause and causes unstable buplex to dissociate
18
Q

How is Bacterial transcription regulated?

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A
  • Polymerase binding and initiation are what is regulated
  • Proteins can bind to promoter to affect gene expression
    • Activator: CRP (cAMP repressor)
    • Repressor: Lac
19
Q

Generally describe eukaryotic transcription

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A
  • Extensive transcript modification
  • Most mRNA encode single gene (monocistronic)
  • Many accessory factors involved
  • Transcription and translation are uncoupled
20
Q

What are the RNA polymerases in eukaryotes and what do they do?

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A

RNA Pol I: synthesize rRNAs
RNA Pol III: synthesize tRNA
RNA Pol II: responsible for synthesis of mRNA

21
Q

What is a CTD?

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A
  • Carboxyl-terminal domain
  • consists of many repeats of a consensus heptad aa sequence (YSPTSPS)
22
Q

What is RNA Pol II important for in Eukaryotes?

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A

RNA Pol II is central to protein coding genes

23
Q

What is a transcription factor?

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A
  • Regulatory proteins that bind to promoters
  • Eukaryotes have complex genomes thus need more proteins
  • Certain transcription factors function as bacterial sigma factors and help recruit RNA Pol to promoters depending on growth conditions
24
Q

Outline the regions involved in transcription (promoter related).

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A
  • TATA box
  • Inr: initiator region/ start site
    • Py n is n# of pyrimidines
  • Promoter: Where TATA Binding Protein binds
    • TBP analogous with sigma 70 in bacteria
25
Outline the steps involved in the loading of transcription factors to Pol II.
- TFIID and TBP bind to TATA - TFIIA and TFIIB bind to complex - TFIIE and TFIIH bind to complex followed by RNA Pol II with other factors - Ribonucleotides are added as needed
26
What happens when the TFs have been loaded and RNA Pol II has attached?
- DNA unwound at Inr region - CTD of Pol II is phosphorylated causing it to escape the promoter and start transcription - Pol II enters elongation phase which releases transcription factors then is enhanced by elongation factors
27
What happens in termination
- Termination is facilitated by termination factors - Elongation factors dissociate, CTD is dephosphorylated as transcription stops and RNA Pol II is released
28
What are some RNA Pol inhibitors?
Actinomycin D - Inhibits elongation in Bact and Euk - Prevents Pol movement Rifampicin - Binds to B subunit of Bact RNA Pol - Prevents promoter clearance step Alpha-Amanitin (from mushroom) - Blocks Pol II and Pol III - Doesnt block it's or Bact's Pol I
29
Describe the RNA processing in Eukaryotes
- Newly synthesized RNA molecule is called Primary transcript - Primary transcript typically includes introns - RNA splicing is when introns are removed and exons are joined together
30
What are the three steps to turn a primary transcript to mRNA?
- 5' Cap is added to protect degredation and aid in translation start - Poly-A tail is added to prolong RNA life - Added by Poly-a Polymerase - Requires a portion of 3' to be removed - Introns removed requires snRNPs
31
What does the CTD of RNA Pol II do?
- Binds mRNA capping - Splices - Binds polyadenylation factors - Terminates transcription
32
Why does splicing result in the formation of a lariat?
When Precursor mRNA is processed, splicing factors will remove an intron and join it with itself forming a lariat and joining the exons to form a mature mRNA
33
What does intron splicing look like?
34
What are the four types of introns?
Group I and Group II - Self splicing - GI found in nuclear mito, chloro genes coding for r/m/tRNA - GII found in transcripts of mito or chrolo mRNA in fungi, plants, algae Spliceosomal introns are spliced by splicosomes - Most common - Found in protein coding region of euk. genome tRNA introns spliced by protein based enzymes - Primary transcripts cleaved by endonuclease - Exons are joined by ATP-dependent ligase
35
What happens to spliceosomal introns?
- Intron removal catalyzed by spliceosome - Forms Lariat of intron and joins the exons
36
Describe the spliceosome.
- Composed of highly conservative RNA proteins (snRNPs) - snRNP contain snRNAs (100-200 nucleotides long in nucl) - snRNAs involved in splicing: U1, U2, U4, U5, U6 - GU at 5' AG at 3' mark sites of splicing
37
What is alternative processing?
When mRNA is processed in more than one way to make different
37
Draw the central dogma of DNA and RNA.
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