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Protein Synthesis > Transcription > Flashcards

Transcription Flashcards

1
Q

Prokaryotic RNA polymerase

A

-multi subunit enzyme which recognizes nucleotide sequence ( promoter region ) at beginning of DNA length to be transcribed and also recognizes termination sequence

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2
Q

What direction is RNA made

A

5-3 antiparallel but complimentary to template ( antisense , minus ) and identical to coding strand ( sense , plus )

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3
Q

How is gene to be transcribed located

A

-through a sequence of nucleotides near gene called promoter region

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4
Q

Prokaryotic RNA POL structure

A

-has core enzyme with 5 subunits
1 2 alpha and omega - enzyme assembly
2 Beta prime - template binding
3 Beta - 5-3 RNA polymerase activity

-has s subunit ( sigma region ) which enables RNA POL to recognize promoter region

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5
Q

What is holoenzyme

A

S region plus core enzyme

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6
Q

Steps in transcription ( simplified )

A

1 initiation
2 elongation
3 termination

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7
Q

What is transcription unit and transcript

A
  • region between termination and promoter

- initial product of transcription

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8
Q

Initiation.

A

-binding of holoenzyme to template ( via beta subunit )forming closed complex and unwinding of dsDNA ( a short length approx 14 bases ) to form open complex called transcription bubble

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9
Q

Consensus sequence

A

-idealized sequence in which bases shown at each Position is base most frequently encountered at that position ie length from initiation site

( not always the case )

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10
Q

Sequences recognized by s factors

A

1 -35 consensus sequence ( 5-TTGACA-3) centered at G 35 bases from initiation site. Initial contact point for Pol and forms closed complex

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11
Q

Numbering of bases left and right to initiation site and reason

A
  • negative if left and positive if right

- regulatory sequence that control transcription are designated by 5-3 sequence on coding strand

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12
Q

Prinbow box

A
  • 2nd consensus site wc holoenzyme moves onto next
  • (-TATAAT-) centered at middle T 10 bases away from initiation site
  • melting of dsDNA occurs here to form open complex transcription bubble
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13
Q

Elongation

A
  • Unwinding continues mediated by POL which then synthesizes transcript from DNA sequence
  • several short RNA strands made and discarded
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14
Q

When does elongation begin

A

When transcript exceeds 10 nucleotides

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15
Q

What happens after transcription done at a specific gene

A

-s subunit released and core can leave promoter and move along template in a processive manner.

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16
Q

What is sliding core of prokaryotic RNA POL

A

Itself

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17
Q

What occurs during transcription between RNA and DNA

A

-short pieces of DNA and RNA bind forming hybrids

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18
Q

How are nucleotides added and you where does energy come from

A
  • ATP dependent which is acquired from triphosphate bonds which beak releasing energy and pyrophosphate
  • nucleotides added with a phosphodiester bond inbetween 3 and 5 OH via ATP hydrolysis
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19
Q

When does transcription stop

A

-at termination signal which can be spontaneous or dependent on rho proteins

20
Q

Rho independent termination

A

-sequence in DNA generates sequence in RNA that is self-complimentary and folds in on itself with a GC rich stem and loop Making a hairpin

21
Q

What is beyond hairpin

A

String of U’s H2 bonded to A’s on DNA strand but weak forces so facilitates separation of RNA from DNA at hybrid

22
Q

Rho protein properties

A

Participation of hexameric Rho protein with ATPase and helicase activities

23
Q

Rho dependent

A

-rho binds with C-rich region in rho recognition site of RNA near 5 end and uses ATPase activity to move along chain it reaches POL paused at termination site and uses ATP dependent helicase active to break hybrid zone

24
Q

Action of antibiotics in prokaryotic RNA synthesis termination

A
  • some antibiotics Prevent bacterial cell growth by inhibiting RNA synthesis
  • Rifampin inhibits transcription by binding to B subunit and prevents chain extension beyond : nucleotides
  • Dactinmyosin binds to DNA template and prevents movement of RNA POL along DNA
25
Q

Difference between Prokaryotic and Eukaryotic Transcription

A
  • eukaryotic cells have multiple RNA POLS for m, r and tRNA
  • have transcription factors
  • each RNA POL in eukaryotes has its one TF and promoters
26
Q

Transcription factors structure and function

A

-large number of multi subunit proteins and are trans proteins

  • required to bind to promoter and regulatory sequences
  • bring POL 2 to promoter site
  • required for transcription complex formation
27
Q

Chromatin requirement for transcription

A

-must be relaxed to allow proteins to access DNA

28
Q

Chromatin structure and gene expression

A
  • histone modifications affect accessibility to DNA

- ATP dependent repositioning of nucleosomes is required to access histones

29
Q

Acetylated and none acetylated histones

A

-if Acetylated then histone positive charge of leucine is cancelled and can’t bond tightly to negative DNA

30
Q

Chromatin remodeling

A

-interconversion between euchromatin and heterochromatin

31
Q

RNA POL’s of eukaryotes

A

1 Pol 1 - synthesis for precursor of 28S ,18S and 5.8S in rRNA in nucleolus

2 Pol 3 - synthesis of tRNA , 5S rRNA and some snRNA and snoRNA

3 Pol 2 - nuclear precursor synthesis of mRNA and also small ncRNA ( miRNA , snoRNA , snRNA )

32
Q

Promoters for RNA POL 2 and function

A
  • sequence is TATAA and similar to Prinbow Box
  • -25 from transcription site
  • called TATA or Hogness box
  • other promoters are Inr ( initiator +1 ) or DPE ( downstream proteins +25 )
  • serve as binding sites for general transcription factors ( GTF ) which interact with each other and Pol 2
33
Q

Cis acting sequences

A

-on same gene as as sequence about to be transcribed

34
Q

General transcription factors

A

Minimal requirement proteins for recognition of promoter , recruitment of pol 2 and initiation of transcription at basal level
-are encoded by diff genes synthesized in cytosol and transit to site of initiation so are trans acting

35
Q

TFIID

A

GTF which recognizes and binds to TATA box and other core promoters ( DPE & Inr )

36
Q

TFIIF

A

Brings pol 2 to promoters

37
Q

TFIIH

A

Melts dsDNA

And clears from promoters by kinase activity phosphorylation polymerase

38
Q

Regulatory elements and transcriptional factors

A

Are upstream of initiation site

-r additional consensus sequences

39
Q

Proximal and distal regulatory consensus sequences

A
  • close ( within 200 nucleotides ) from site of initiation
  • elements such as CAAT and GC box

-further ( beyond 200 ) and include enhanced elements

40
Q

Specific transcription factors

A

-bind to 2 domains
1 DNA binding domain
-bind to promoter proximal elements to regulate frequency of initiation
-bind to distal to mediate responses to hormones and regulate which genes are expressed

2 transcription activation domain ( recruits GTF to core promoter and coactivator Proteins

41
Q

CTF and Sp1

A
  • CAAT box transcription factor ( STF binds to CAAT box )

- binds go GC box ( specificity factor 1 )

42
Q

Motifs by which TF’s bind to DNA

A

Zinc fingers
Leucine loops
Helix loop helix

43
Q

Role of enhancers

A

Have sequences called response elements that bind to STF

44
Q

DNA bending

A

-causes ehancer elements far from promoters to be closer and interact with transcription factors stimulating and regulating gene expression

45
Q

Silencers

A

Also affect transcription from afar by inhibit it

46
Q

Inhibitors of RNA polymerase 2

A

A-amanitin ie poison form death cap ( potent toxin ) mushroom Amaita Phalloides form tight complex with Pol 2 and inhibits mRNA synthesis s

Protein Synthesis (8 decks)

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