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

Gene Transcription & RNA modification (part 2) Flashcards

1
Q

After ________ is assembled into its six subunits it binds loosely to the DNA & slides along the DNA looking for the promoter

A

RNA polymerase holoenzyme

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2
Q

Once the RNA polymerase holoenzyme finds the promoter what happens?

A

The sigma factor recognizes both the -35 & -10 sequences & its helix turn - helix motif allows it to bind tightly to those sequences

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3
Q

Describe the initiation process in bacterial transcription?

A
  1. Holoenzyme scans DNA & sigma factor recognizes promoter & binds tightly to it
  2. A close complex is formed
  3. Short RNA is made in the open complex where the sigma factor is released
  4. Core enzymes elongates
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4
Q

The process of _________ is initiated when the sigma factor within holoenzyme binds to the promoter to form a closed complex

A

Transcription

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5
Q

In the ________ the strand of DNA in the promoter region are not separated

A

Closed Complex

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6
Q

So to actually begin transcription in bacteria what must happen?

A

The double-stranded DNA must be unwinded by DNA helicase to form a open complex

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7
Q

Where does the unwinding of DNA begin at?

A

The TATAAT or TATA box region because its easier to break A-T bonds since it only has 2 hydrogen bonds

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8
Q

Sigma binding occurs in the ________ where the DNA is still double stranded

A

Close complex

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9
Q

TATA box unwinding occurs in the ________ to actually start transcription

A

Open complex

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10
Q

__________RNA is made in the open complex & when the sigma factor is released initiation ends

A

Nascent RNA

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11
Q

The RNA transcript is synthesized during __________ stage

A

Elongation Stage

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12
Q

The mRNA is made in the ________ direction with no proof reading

A

5’ to 3’ direction

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13
Q

Template strand

A

DNA strand that is used as a template for RNA synthesis (antisense strand)

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14
Q

Coding Strand

A

Strand being formed by using the template strand (sense strand & uses U instead of T)

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15
Q

RNA follow what base rules?

A

A-U & G-C

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16
Q

The template strand is read in the 3’ to 5’ direction but mRNA is made in the __________ direction

A

5’ to 3’ direction

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17
Q

The location of the template strand can affect the ______ mRNA is made where if the top strand is the template strand then it is made from right to left but if the bottom strand is use then its made from left to right ( so transcription can occur in opposite directions)

A

Direction

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18
Q

Transcription is terminated by either an __________ or a ___________

A

RNA binding protein or intrinsic terminator

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19
Q

Describe the elongation stage

A
  1. RNA polymerase slides along the DNA creating an open complex as it moves
  2. The template strands is used to make complementary copy of RNA as RNA-DNA hybrid
  3. RNA polymerase moves along the template strand in a 3’-5’ direction & mRNA is made in the 5’-3’ direction
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20
Q

_________ occurs when the short RNA-DNA hybrid region is forced to separate & release new mRNA & RNA polymerase

A

Termination

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21
Q

_________ ends elongation

A

Termination

22
Q

What are the two different mechanism of termination in E. Coli?

A
  1. p (rho)-dependent

2. p(rho)-independent

23
Q

In p(rho) dependent termination what happens?

A

The termination requires a protein to end termination

24
Q

What are the 2 sequences that p(rho) dependent termination need?

A
  1. Rut Site (rho utilization site)

2. p(rho) protein

25
Q

Rut site acts as a recognition site for ________

A

rho (p) protein

26
Q

The ________ acts as a helicase & separates the RNA-DNA hybrid region

A

rho (p) protein

27
Q

Describe the rho(p) dependent termination process

A
  1. p recognition site on the mRNA allows the rho (p) protein to bind to the rut site on the mRNA & move toward the 3’ end
  2. RNA polymerase trancribes a region that forms a stem loop & proceeds to the terminator . The stem loop cause RNA polymerase to pause
  3. While its paused the rho (p) protein catches up to the open complex & separates the RNA -DNA hybrid & the complete RNA strand & RNA polymerase is released
28
Q

rho (p) independent (or intrinsic) termination

A

Doesn’t require rho (p) protein

29
Q

What are the two sequences (regions) in rho (p) independent?

A
  1. U rich region at 3’ which has weak A-U bonds

2. Stem loop before U rich region

30
Q

Describe rho (p) independent process

A
  1. Stem loop causes RNA polymerase to pause & NusA stabilizes the pausing
  2. While RNA polymerase is paused the weak bonded U rich sequences is not bale to hold the RNA-DNA hybrid together & is termination occurs by it falling apart
31
Q

Gene transcription in eukaryotes is similar to bacterial gene transcription but more _______

32
Q

Why is eukaryote gene transcription more complex?

A

Its larger, contain organelles & is multicellular

33
Q

What are the 3 different types of RNA polymerase used in eukaryote gene transcription?

A
  1. RNA polymerase 1
  2. RNA polymerase 2
  3. RNA polymerase 3
34
Q

RNA polymerase 1

A

Transcribes all of the genes for ribosomal RNA (rRNA)

35
Q

RNA polymerase 2

A

Transcribe all protein-encoding genes so its responsible for the synthesis of mRNA which leads to translation

36
Q

RNA polymerase 3

A

Transcribes all the genes for tRNA (transfer RNA) & leads to translation

37
Q

RNA polymerase in prokaryotes & eukaryotes have a _______ shape

A

Hand Shape

38
Q

Eukaryotic protein encoding genes have a _________ & _________

A

Core promoter & regulatory elements

39
Q

What are the 2 features found in most promoters ?

A
  1. Core promoter

2. Regulatory sequences

40
Q

Core promoter

A

Short DNA sequence that is necessary for transcription to take place, it contains TATA box & transcriptional star site where transcription begins

41
Q

Core promoter produces what?

A

Basal transcription- produces low level of transcription & has no regulatory sequence

42
Q

Regulatory sequences

A

Short DNA sequences that affect the ability of RNA polymerase to recognize the core promoter & also where regulatory proteins bind to

43
Q

What are the two types of regulatory sequences?

A
  1. Enhancer

2. Silencer

44
Q

Enhancer

A

Are activating sequences that are need to stimulate transcription

45
Q

Silencers

A

Prevent transcription of a gene

46
Q

Regulatory sequence are found between _______ & _______

A

-100 & -50

47
Q

TATA Box, enhancers, & silencers are all _________ factors

A

Cis-acting Factors

48
Q

What are the two factors that control transcription?

A
  1. Cis-acting factor

2. Trans-acting factor

49
Q

Cis-acting factor

A

Are always on the same molecule as the gene they regulate & they regulate themselves (used for DNA sequences)

50
Q

Trans-acting factor

A

Binds to cis acting factor & regulates others, they are on a different molecule from the gene they regulate (use for proteins)

51
Q

RNA polymerase & regulatory proteins are __________

A

Trans-factors

52
Q

Transcription of eukaryotic protein encoding genes is initiated when ________ & __________ factors bind to a promoter sequence

A

RNA polymerase 2 & general transcription factors

Biology (64 decks)

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