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Gene Transcription & RNA modification pt 2 (2) Flashcards

1
Q

Describe the initiation stage of bacterial transcription

A
  1. After sliding along the DNA, the sigma factor recognizes a promoter & RNA polymerase holoenzyme forms a closed complex
  2. An open complex is formed & short RNA is made
  3. Sigma factor is release & the core enzyme is able to move along the DNA & make RNA (mRNA)
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2
Q

The RNA transcript (mRNA) is made during __________ stage

A

Elongation Stage

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3
Q

Template strand (antisense strand)

A

The DNA strand that is a template for RNA synthesis

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4
Q

In RNA synthesis A binds to what?

A

U (G-C)

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5
Q

mRNA is made in ________ direction with no proofreading

A

5’ to 3’ direction

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6
Q

Transcription can occur in _______ direction depending on which strand is the template strand, if the bottom strand is the template then transcription occurs from left to right but if the top strand is the template then it occurs from right to left

A

Opposite direction

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7
Q

Describe the elongation stage in bacterial transcritption

A
  1. RNA polymerase slides along the DNA creating an open complex as it moves
  2. The template strand is used to make a complementary copy of RNA resulting in an RNA-DNA hybrid
  3. RNA polymerase moves along the template strand in a 3’ to 5’ direction & RNA is synthesized in the 5’ to 3’ direction
  4. The complementary rule is A-U/ G-C in RNA
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8
Q

Bacterial transcription is terminated by either an _________ or _________

A

RNA - binding protein or intrinsic terminator

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9
Q

Termination

A

End of RNA (mRNA) synthesis

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10
Q

__________ occurs when the RNA-DNA region is forced to sperate which releases the new RNA transcript (mRNA)

A

Termination

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11
Q

In E. coli (bacteria) what are the 2 different mechanisms for termination?

A
  1. rho (p) - dependent model (termination)

2. rho (p) - independent model (termination)

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12
Q

rho (p) - dependent model (termination)

A

Require the use of p -protein to end transcription

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13
Q

What are the 2 sequences in rho-dependent termination?

A
  1. A sequences from the terminator called rut site which acts as a recognition site for binding rho (p) proteins to mRNA
  2. Stem loop region, where the stem loop forms from complementary sequences which causes RNA polymerase to puase the synthesis of mRNA which allows the p-protein to catch up to the stem loop & past it to break the hydrogen bonds between DNA & RNA
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14
Q

The _______ functions as a helicase & separates the RNA -DNA hybrid region (binds to rut site & moves towards the 3’ end)

A

p- protein

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15
Q

rho (p) independent (intrinsic) termination

A

Doesn’t need p- protein

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16
Q

What are the two sequences in rho-independent termination?

A
  1. U-A (U rich region) bonds at the 3’ that has weak U-A bonds
  2. Stem loop
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17
Q

Describe the rho-independent termination process?

A
  1. Stem loop stalls RNA polymerase, NusA stabilizes the pausing
  2. While RNA polymerase pauses the weakly bound U-rich sequences is not able to hold the RNA-DNA hybrid together, termination occurs by RNA polymerase & mRNA falling off
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18
Q

Describe the process of rho-dependent termination

A
  1. p protein binds to the rut site in RNA & moves towards the 3’ end
  2. RNA polymerase transcribes a region that forms a stem loop & the stem loop causes RNA polymerase to pause
  3. During the pause the p protein catches up to the open complex & seperates the RNA-DNA hybrid
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19
Q

Transcription in ________ is more complex because it is larger, has organelles & is multicellular

A

Eukaryotes

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20
Q

What are the 3 RNA polymerase in Eukaryotes?

A
  1. RNA polymerase 1
  2. RNA polymerase 2
  3. RNA polymerase 3
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21
Q

RNA polymerase 1

A

Transcribe all of the genes for ribosomal RNA (rRNA) (translation)

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22
Q

RNA polymerase 2

A

Transcribe all protein-encoding genes, therefore responsible for synthesis of mRNA (messenger RNA)

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23
Q

RNA polymerase 3

A

Transcribe all the genes for tRNA (transfer RNA) (translation)

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24
Q

Both RNA polymerase in prokaryotes & eukaryotes have the same shape which is a ________

A

Hand Shape

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25
Eukaryotic structural genes have a _______ & _________
Core promoter & regulatory sequences
26
What are the 3 regions eukaryotic structural genes have in the promoter?
1. Regulatory sequences 2. TATA Box 3. Transcriptional start site
27
Core promoter
Short DNA sequence that is need for transcription & it contains the TATA box & transcriptional start site
28
Basal transcription
When low level of transcription is produce (core promoter produces low level of transcription)
29
_________ are short DNA sequences that affect RNA polymerase to recognizes the core promoter & begin transcription
Regulatory Sequences
30
What are the two categories to regulatory sequences?
1. Enhancers | 2 Silencers
31
Enhancers
Activating sequences that stimulate transcription
32
Silencers
DNA sequences that prevents transcription
33
What is the common location for regulatory sequences?
-50 to -100 region
34
Cis acting factors
Regulates itself & is on the same chromsome (molecule) as the gene they regulate
35
TATA box (promoter) , enhancers, & silencers are all __________
Cis- acting factors
36
Trans-acting factors
Bind to cis-factors & regulate others on different molecule than the gene
37
____________ of eukaryotic structural gene is initiated when RNA polymerase 2 & 5 general transcription factors (GTF) bind to a promoter sequence (does it without regulatory genes)
Transcription (Basal Transcription)
38
Describe the initiation process in eukaryotic transcription
1. TFIID binds to the TATA box 2. TFIID binds to TFIIB 3. TFIIB promotes the binding of RNA polymerase 2 & TFIIF to core promoter 4. TFIIE & TFIIH bind to the complex which forms a closed complex called - preinitiation complex (PIC) 5. TFIIH acts as a helicase & unwinds DNA & it also act as a kinase & phosphorylates the tail of RNA polymerase 2 6. TFIIB, TFIIE, & TFIIH is release to make an open complex
39
_____________ of RNA polymerase 2 occurs after the 3' end of the transcript (mRNA) is cleaved near the polyadenylation signal sequence at the 5' end
Eukaryotic transcriptional termination
40
What are the two mechanism used in eukaryotic transcription termination?
1. Allosteric termination | 2. Torpedo termination
41
Allosteric termination (shape change)
RNA polymerase 2 becomes destabilized after it has transcribe the polyadenylation signal sequence & it falls off DNA
42
Torpedo termination
RNA polymerase 2 is physically removed from the DNA where it is cleaved by exonuclease & it binds to the other half of RNA (mRNA) & transcript is degraded in the 5' to 3' direction & RNA polymerase falls off from the DNA
43
Describe the eukaryotic termination steps
1. RNA polymerase 2 passes polyA signal sequence 2. RNA is cleaved past polyA signal 3. Torepdo model or allosteric model is used
44
RNA modification
Occurs after transcription, where: •rRNA remove spacers •tRNA add CCA •mRNA is cap, splice, & polyadenylate edit
45
rRNA (rRNA modification makes it go from long to short)
Located in the nucleolus & is: 1.transcribed 2. processed 3. bound to ribosomes
46
What happens with 45S genes?
After transcription it forms pre-rRNA which is processed in the nucleolus & forms 3 products that bind to ribosomes
47
tRNAs (modification makes it goes from long to short)
1. both ends digested 2. CCA to 3’ 3. modify nucleotides
48
What are the modified nucleotides (bases) in tRNA?
1. mG = Methylguanosine 2. P = Pseudouridine 3. T = 4-Thiouridine 4. IP = 2- Isopentenyladenosine
49
mRNAs
1. modified in nucleus 2. spliced 3. capped 5’ end 4. poly-A at 3' end
50
Prokaryotes are _________
Co-linear
51
Co-linear
Contains the same info from the gene to protein
52
Eukaryotes are not co-linear because they are involved in _________
Splicing
53
Splicing
Occurs during transcription, the introns in pre-mRNA are splice & exons are connected by phosphodiester bonds to make a mature mRNA
54
Splicing removes all the ________ and some _______
Intron, exons
55
What are the 3 mechanisms for splicing?
1. Group 1 2. Group 2 3. Spliceosome
56
Group 1 & 2 splicing
Are self-splicing where they don't need an enzyme & mRNA a ribozyme
57
Describe group 1 splicing
The splicing of group I introns involves the binding of a free guanosine to a site within the intron, leading to the cleavage of RNA at the 3′ end of exon 1. The bond between a different guanine nucleotide (in the intron strand) and the 5′ end of exon 2 is cleaved. The 3′ end of exon 1 then forms a covalent bond with the 5′ end of exon 2 which forms a mature mRNA
58
Spliceosome
Is a large complex which contains RNAs & proteins
59
Spliceosome binds ________ | boundary which gives it the correct orientation (catalyze reaction)
Intron-exon
60
Describe the process of splicing with spliceosome
1. U1 binds to the splice site 2. U2 binds to the branch site 3. Other proteins bind which causes introns to loop out & exons are brought together 4. The 1st splice site is cut & introns connect to the branch site to form a lariat 5. 2nd splice site is cut & exons connect & introns are released & degraded

Biology (64 decks)

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