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M!cr0 G3n3t!cs > Transcription > Flashcards

Transcription Flashcards

1
Q

Creation of complementary mRNA sequences from short strands of DNA

A

Transcription

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2
Q

Which strand of DNA is transcribed and in what direction

A

Template strand; 5’ to 3’

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3
Q

3 major components need in transcription

A
  1. a DNA template
  2. Raw materials or substrates for RNA
  3. Transcription apparatus consisting of enzymes to catalyze RNA synthesis
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4
Q

Transcription starts when enzymes recognize the _________ and ends at the _________. In between is the ______ of the gene which is copied into an RNA molecule

A

Promoter region; Terminator region; RNA-coding region

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5
Q

In terms of direction, upstream refers to the what end of the DNA

A

5’-end

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6
Q

The mRNA is complementary and antiparallel to the ____ strand

A

Template

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7
Q

Bacterial RNA polymerase has _ alpha, _ beta, _beta prime, and _ omega

A

2,1,1,1

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8
Q

It joins and leaves the core enzymes as it is needed forming a holoenzyme. It recognizes a specific promoter region for every particular gene

A

Sigma factor

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9
Q

_______ are antibiotics that target bacterial RNA polymerases. Commonly used as cures against______

A

Rifamycins; Tubercolosis

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9
Q

True or False: An RNA polymerase without a sigma factor will not bind to any part of the genome

A

False

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10
Q

Define the mechanistic action of rifamycin

A

Binds to the part where the RNA polymerase should bind to the DNA

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11
Q

Enumerate the phases of transcription

A
  1. Initiation phase
  2. Elongation Phase
  3. Termination Phase
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12
Q

Enumerate the phases of initiation

A

-Promoter recognition
-Formation of the transcription bubble
-Creation of first bonds between rNTPs
-Escape of transcription apparatus from the promoter

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13
Q

Promoters have different affinities for RNA polymerase. Give a consequence/advantage of these differences

A

These differences lead to variations on frequency and prioritization of expression of genes.

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14
Q

Are short sequences of considerable similarity found in promoter regions

A

Consensus sequence

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15
Q

The most common consensus sequence in prokaryotes

A

Pribnow box or -10 consensus sequence

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15
Q

Give an example of a specific sequence in Pribnow box/ -10 consensus sequence

A

TATAAT

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16
Q

True or False: Pribnow box is always TATAAT

A

False

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17
Q

A consensus sequence in prokaryotes that control the rate of transcription

A

-35 consensus sequence

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18
Q

Difference between down mutation and up mutation

A

Rate of transcription (Down= Reduce, Up=Increase)

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19
Q

Unwinding of gene beings at the ___ consensus sequence and extends downstream covering ___ to ___ sites

A

-10; -12: +12

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20
Q

How much nucleotides are transcribed as initial abortive attempts before proceeding to the elongation phase?

A

2-6 nucleotides

21
Q

True or False: During elongation, the sigma subunit should always be released regardless of the type of RNA

A

False; Should be either depending on the type of RNA

22
Q

During elongation phase, the leading edge is found in what direction. In what direction does the trailing edge found?

A

Downstream= Leading edge
Upstream= Trailing edge

23
Q

Which is faster, the transcription of bacteria or eukaryotes? Describe the magnitude of their difference

A

Eukaryotes are faster having 1000-2000 nucleotides per second while prokaryotes have 40 nucleotides per second

24
Q

In Elongation phase, it is around 18 nucleotides in length of unwound DNA where the mRNA is continuously synthesized

A

Transcription bubble

25
Q

Negative supercoiling is found upstream of downstream?

A

Upstream

26
Q

Enzyme that relieves the stress associated with unwinding and rewinding of DNA

A

Topoisomerase

27
Q

True or False. Termination phase is an abrupt stop

A

False

28
Q

Enumerate the process of termination phase

A

-RNA polymerase stops synthesizing RNA
-RNA molecules is released from RNA polymerase
-Newly made RNA dissociates from the DNA
-The RNA polymerase detaches from DNA

29
Q

Enumerate the process of Rho-dependent termination

A

-Rho protein binds to the binding site of the unstructured RNA and moves toward its 3’-end
-Rho protein has helicase activity that unwinds RNA-DNA hybrid in the transcription bubble
The RNA polymerase pauses when it encounters the terminator site, then the rho protein to catches up

30
Q

Type of terminators in prokaryotes that contains inverted repeats that form hairpins when transcribed into mRNA

A

Rho-independent terminators

31
Q

Explain the process of Rho-independent terminators

A

-Inverted repeats are followed by 7-9 A positions that convert to a string of U
-The hairpins serve as blocks to destabilize the DNA-RNA pairings
-The weak A-U string pairing facilitates the separation of DNA and RNA

32
Q

Polycistronic mRNA is common in _____ while monocistronic is common in _______

A

Prokaryotes; Eukaryotes

33
Q

Define the functions of the following bacterial RNA polymerase:
-RNA Polymerase I
-RNA Polymerase II
-RNA Polymerase III
-RNA polymerase IV and V

A

-For RNA transcription
-For transcribing pre-mRNAs, snoRNAs, some miRNAs, and some snRNAs
-Transcribing other small RNA molecules (tRNAs, small rRNA, and some miRNAs and snRNAs)
-Transcribe RNAs that play roles in DNA methylation and chromatic structure in plants

34
Q

In Eukaryote Transcription, they assemble near the start site of a gene to initiate minimal levels of transcription together with the RNA polymerase

A

General Transcription Factors

35
Q

This is the combination of general transcription factor and RNA polymerase in eukaryote transcription

A

Transcriptional Activator Apparatus

36
Q

In eukaryote transcription, this stimulates formation of the basal transcription apparatus at the start site of a gene

A

Transcriptional Activator Proteins

37
Q

In eukaryote transcription, this is where the basal transcription apparatus binds and located upstream of the gene

A

Core promoter

38
Q

In eukaryote transcription, it is composed of TATAAA and is found -25 to -30bp upstream of the start site

A

TATA box

39
Q

in eukaryote transcription, these are located immediately upstream to core promoters and where transcriptional activator proteins binds. These mostly affect rate of transcription

A

Regulatory Promoters

40
Q

More distant upstream sequences in eukaryote transcription; These sites often loop out so that these can directly connect to the basal activator protein at the core promoter

A

Enhancers

41
Q

Where do the protein complex attach?
Basal Transcription Apparatus:
Transcriptional Activator Proteins:

A

Basal Transcription Apparatus: Core promoters
Transcriptional Activator Proteins: Regulatory promoters and Enhancers

42
Q

Sigma factor of prokaryotes is what of eukaryotes?

A

Transcription factors

43
Q

What trasncription factor recognizes the TATA box with its TATA-binding protein?

A

TFIID

44
Q

In eukaryote transcription, this is formed when the single-stranded DNA is positioned within the active site of the RNA polymerase

A

Open complex

45
Q

Elongation starts at ___bp from the start site when the transcription factors separate for re-use in other transcription events

A

30bp

46
Q

True or False. RNA Polymerase I in Eukaryote Transcription is similar to rho-dependent termination in Bacteria

A

True

47
Q

In RNA polymerase I termination, it requires a _________ but it binds to a sequence ________ of the stop site

A

Termination Factor; Downstream

48
Q

True or False. RNA Polymerase III termination is similar to the Rho-dependent termination in bacteria

A

False

49
Q

Difference between RNA polymerase III and the Rho-independent termination of Bacteria

A

Lack of hairpin structure after string of U

50
Q

Describe the series of event in RNA polymerase II termination

A

-Transcription continues well beyond the termination site producing a pre-mRNA
-The pre-mRNA is cleaved at a consensus site which separates from the excess non-coding part by the Rat1
-Rat 1 proceeds to degrade until it reaches the transcription machinery

51
Q

Archaea RNA polymerase recognizes TATA-box using what transcription factor?

A

TFIIB

M!cr0 G3n3t!cs (3 decks)

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