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Biology > Gene Transcription & RNA modification pt 2 (2) > Flashcards

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
Q

Eukaryotic structural genes have a _______ & _________

A

Core promoter & regulatory sequences

26
Q

What are the 3 regions eukaryotic structural genes have in the promoter?

A
  1. Regulatory sequences
  2. TATA Box
  3. Transcriptional start site
27
Q

Core promoter

A

Short DNA sequence that is need for transcription & it contains the TATA box & transcriptional start site

28
Q

Basal transcription

A

When low level of transcription is produce (core promoter produces low level of transcription)

29
Q

_________ are short DNA sequences that affect RNA polymerase to recognizes the core promoter & begin transcription

A

Regulatory Sequences

30
Q

What are the two categories to regulatory sequences?

A
  1. Enhancers

2 Silencers

31
Q

Enhancers

A

Activating sequences that stimulate transcription

32
Q

Silencers

A

DNA sequences that prevents transcription

33
Q

What is the common location for regulatory sequences?

A

-50 to -100 region

34
Q

Cis acting factors

A

Regulates itself & is on the same chromsome (molecule) as the gene they regulate

35
Q

TATA box (promoter) , enhancers, & silencers are all __________

A

Cis- acting factors

36
Q

Trans-acting factors

A

Bind to cis-factors & regulate others on different molecule than the gene

37
Q

____________ 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)

A

Transcription (Basal Transcription)

38
Q

Describe the initiation process in eukaryotic transcription

A
  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
Q

_____________ of RNA polymerase 2 occurs after the 3’ end of the transcript (mRNA) is cleaved near the polyadenylation signal sequence at the 5’ end

A

Eukaryotic transcriptional termination

40
Q

What are the two mechanism used in eukaryotic transcription termination?

A
  1. Allosteric termination

2. Torpedo termination

41
Q

Allosteric termination (shape change)

A

RNA polymerase 2 becomes destabilized after it has transcribe the polyadenylation signal sequence & it falls off DNA

42
Q

Torpedo termination

A

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
Q

Describe the eukaryotic termination steps

A
  1. RNA polymerase 2 passes polyA signal sequence
  2. RNA is cleaved past polyA signal
  3. Torepdo model or allosteric model is used
44
Q

RNA modification

A

Occurs after transcription, where:
•rRNA remove spacers
•tRNA add CCA
•mRNA is cap, splice, & polyadenylate edit

45
Q

rRNA (rRNA modification makes it go from long to short)

A

Located in the nucleolus & is: 1.transcribed

  1. processed
  2. bound to ribosomes
46
Q

What happens with 45S genes?

A

After transcription it forms pre-rRNA which is processed in the nucleolus & forms 3 products that bind to ribosomes

47
Q

tRNAs (modification makes it goes from long to short)

A
  1. both ends digested
  2. CCA to 3’
  3. modify nucleotides
48
Q

What are the modified nucleotides (bases) in tRNA?

A
  1. mG = Methylguanosine
  2. P = Pseudouridine
  3. T = 4-Thiouridine
  4. IP = 2- Isopentenyladenosine
49
Q

mRNAs

A
  1. modified in nucleus
  2. spliced
  3. capped 5’ end
  4. poly-A at 3’ end
50
Q

Prokaryotes are _________

A

Co-linear

51
Q

Co-linear

A

Contains the same info from the gene to protein

52
Q

Eukaryotes are not co-linear because they are involved in _________

A

Splicing

53
Q

Splicing

A

Occurs during transcription, the introns in pre-mRNA are splice & exons are connected by phosphodiester bonds to make a mature mRNA

54
Q

Splicing removes all the ________ and some _______

A

Intron, exons

55
Q

What are the 3 mechanisms for splicing?

A
  1. Group 1
  2. Group 2
  3. Spliceosome
56
Q

Group 1 & 2 splicing

A

Are self-splicing where they don’t need an enzyme & mRNA a ribozyme

57
Q

Describe group 1 splicing

A

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
Q

Spliceosome

A

Is a large complex which contains RNAs & proteins

59
Q

Spliceosome binds ________

boundary which gives it the correct orientation (catalyze reaction)

A

Intron-exon

60
Q

Describe the process of splicing with spliceosome

A
  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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