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BIO282 > Gene Expression - Transcription > Flashcards

Gene Expression - Transcription Flashcards

1
Q

Transcription Definition

  • Coding vs Template strand
  • Promoter region
A
  • Process whereby DNA is copied to RNA
  • RNA always synthesised in a 5’ to 3’ direction (RNA polymerase adds bases to 3’ end)

Template strand: RNA polymerase uses this strand as a template to build the mRNA transcript

Coding strand: Has same sequence as RNA (but with T’s instead of U’s)

Promoter region = -10 and -35 bases from gene (upstream)

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2
Q

2 ways transcription is terminated

A
  1. Rho Dependent termination: Protein called Rho (hexose) binds at Rut site and pulls RNA from RNA polymerase
    - energy gotten from ATP hydrolysis
    - is a well defined process - there is a specific place that Rho protein can bind
  2. Rho independent termination: termination by hairpin loop formation (due to inverted repeats)
    • U’s at end of hairpin (serve as signal for RNA polymerase release)
    • causes a decrease in the affinity between RNA polymerase and the DNA (lots of U’s mean only A-U bonds holding them together = weak (has only 2 H bonds))
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3
Q

Numbers of RNA polymerases in Bacteria, Plants & Eukaryotes

A

Bacteria; 1 type of RNA polymerase
Plants; 5 types of RNA polymerase
Eukaryotes; 3 Types of RNA polymerase
-these have divided the jobs

rRNA = RNA polymerase 1
pre-mRNA = RNA polymerase 2
small RNA = RNA polymerase 3

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4
Q

RNA polymerase 1 - UPE, UPF & core element

A
  • RNApolymerase 1 transcribes rRNA precursor gene
    • core element -45 to +20
    • upstream promoter element (UPE) = -180 to -107
  • gene present in 100s of copies in cell
  • rRNA make ribosomes
  • Upstream promoting factor (UPF) binds to UPE to increase ability of core binding actor to bind to core promoter
    • for core promoter to bind, need protein to bind upstream

-Core binding factor consists of 4 proteins including Tata box binding protein) - required for initiation by RNA plymerase 2 & 3 also

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5
Q

RNA polymerase 3

A
  • exception to rule that promoter region is upstream of gene
    • has promoters w/in genes (2 out of 3 types do)
  • all transcribe small RNAs (i.e. tRNA, small nuclear RNA)
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6
Q

RNA polymerase 2

A
  • Is the main one - transcribes genes that get translated later
  • many different types of promoters - have different types of control mechanisms (i.e. TATA box, GC box)
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7
Q

Gene Expression

Gene

*Important note about reading nucleic acids

A

Gene expression: is the flow of genetic information from DNA via RNA (transcription) to protein (translation)

Gene: Part of DNA that gets transcribed into an RNA

*A nucleic acid only makes sense if read in 5’ to 3’ direction

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8
Q

2 types of RNAs produced (classification)

-enzyme that synthesizes RNAs

A
  1. Informational RNAs - contain messages of amino acid sequence of proteins (get translated into proteins)
  2. rRNAs, tRNAs, snRNAs, scRNAs - are not translated into proteins - are functional

Enzyme that sysnthesises RNAs = RNA polymerase

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9
Q

2 ways transcription is terminated

A
  1. Rho Dependent termination: Protein called Rho (hexamer - 6 subunits) binds at Rut site and pulls RNA from RNA polymerase
    - energy gotten from ATP hydrolysis
    - is a well defined process - there is a specific place that Rho protein can bind
  2. Rho independent termination: termination by hairpin loop formation (due to inverted repeats)
    • U’s at end of hairpin (serve as signal for RNA polymerase release)
    • causes a decrease in the affinity between RNA polymerase and the DNA (lots of U’s mean only A-U bonds holding them together = weak (has only 2 H bonds))
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10
Q

Bacterial RNA polymerase

  • Core element (5 subunits & function)
  • Holoenzyme - what factor joins
A

-Bacteria possess only 1 type of RNA polymerase that catalyses all classes of RNA
Core element (5 subunits):
-2 x alpha (enzyme assembly, promoter recog.)
-beta (Catalytic centre)
-beta prime (Catalytic centre)
-omega (provides stability of enzyme)

*Sigma factor joins to core to form holoenzyme (promoter specificity)

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11
Q

Transcription Unit

-composition (3)

A

Transcription unit: stretch of DNA that encodes an RNA molecule & sequence necessary for its transcription

Composed of; -

  • Promoter
  • RNA coding sequence
  • Terminator
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12
Q

Promoter Region

  • 3 parts
  • Consensus sequence (definition)
A

[Bacteria]
-Typical promoter has 3 components; consensus sequences at -35 and -10 and the start point (which is a purine 90% of time)

  • 10 sequence = TATAAT
  • 35 sequence + TTGACA

Consensus sequences: consists of most commonly encountered bases at each position in a group of related sequences

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13
Q

Stages of Transcription

A

Initiation -> Elongation -> Trmination

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14
Q

RNA polymerase Action during stages of transcription

A
  • RNA polymerase binds to promoter and melts DNA, remains stationary during initiation
  • Moves along template during elongation
  • Dissociates at termination
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15
Q

Eukaryotic RNA polymerases - number

A

-Eukaryotic cells contain 5 types of RNA polymerases - 4th and 5th found in plants

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16
Q

RNA polymerase 1 (eukaryotes)

  • 2 critical regions in promoter
  • what it transcribes
A
  • Transcribes the rRNA precursor gene (hundreds of copies in each cell)
  • promoter has 2 critical regions: core element (located -45 to +20) and Upstream promoter element (-180 to -107)
  • transcription units for RNA polymerase 1 have a core promoter separated by approx 70 bp from the upstream promoter element
    • space between these two elements crucial for proper transcription
  • Upstream binding factors bind to Upstream promoter element to increase the ability of core-binding factor to bind to core promoter (consists of 4 proteins)
17
Q

RNA polymerase 2 (Eukaryotes)

  • what it transcribes
  • what the genes have
A
  • Transcribes pre-mRNA, snoRNAs, some miRNA 7 some snRNAs
  • Genes transcribed have core promoter region and regulatory promoter w/ conserved sequences
  • Minimal pol 2 Promoter has a TATA box approx 25 bp upstream of InR
    • TATA box has consensus seq. of TATAAA
  • promoters also contain short sequences where regulatory protein bind and control gene expression
18
Q

RNA Polymerase 3 (Eukaryotes)

A

-Transcribes tRNA and other small rRNA

19
Q

Termination of Transcription (in eukaryotes) for different polymerases

A
  • RNA polymerase 1: 18 bases terminator sequence 1kb downstream - accessory factor required
  • RNA polymerase 2: polyadylation of mRNA
  • RNA polymerase 3: Terminator region similar to prokaryotic terminator - termination occurs at a run of 4Us locatd w/in rich GC region

*hairpin structures do not appear to be involved in termination of RNA polymerases 1 or 3

BIO282 (17 decks)

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