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Biochem K > Transcription (Mol. Bio.) > Flashcards

Transcription (Mol. Bio.) Flashcards

1
Q

Which are the general steps of the synthesis of a primary transcript?

A
  • Initiation
  • Elongation
  • Termination
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2
Q

What regulates the Initiation of transcription?

A
  • A number of DNA regions, generally located upstreams from the initiation site.
  • Protein Factors which bind to these sequences.
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3
Q

What does modulation of the transcription process result in?

A

Altered rates of protein synthesis and metabolic & phenotypic changes (Adaption)

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4
Q

Which are the two major classes of RNA?

A
  • Non protein coding

- Protein coding

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5
Q

Subdivision of Non Protein coding RNA ?

A

Large: rRNA, lncRNA
Small: sncRNA, siRNA, miRNA

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6
Q

Which RNA’s are directly and indirectly involved in Transcription, respectively?

A

Directly: mRNA, tRNA, rRNA
Indirectly: the rest

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7
Q

The role of snRNA in transcription

A

RNA splicing

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8
Q

The role of siRNA and miRNA in transcription?

A

Altering the mRNA function for modulation of gene expression

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9
Q

The role on lnRNA in transcription?

A

Gene expression participation

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10
Q

Which are the similarities between DNA and RNA synthesis?

A

1) the general steps of Initiation, elongation and Termination
2) Both have large multicomponent Initiation complexes

3) polrity 5’-3’
4) Base pairing

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11
Q

Which are the differences between DNA synthesis and RNA synthesis?

A

1) ribo/deoxy ribe sugars
2) T/U bases
3) RNA synthesis doesnt require a primer, nor a Primase
4) DNA whole/ RNA a piece of DNA copied
5) Transcription has no highly active proofreading function

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12
Q

Which Enzyme catalyses the transcription in Prokaryotic cells?

A

DNA dependent RNA-Polymerase: Catalyses formation of rRNA,tRNA and mRNA - all types of RNA really.

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13
Q

What are the subunits of the core which the RNAP is made up of, and what are their roles?

A

1 beta subunit : responsible for catalysing the RNA strand. Binds to Mg2+
1 Beta prime unit: binds to DNA (Clamp)
2 alpha subunits: recognises regulatory factors

(also has a (w) subunit apparently but no function mentioned.

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14
Q

What is the sigma factor?

A

An initiator protein that binds to the core of RNA pol. and felps it locate the promotor regions which is needed for initiation of transcription in prokaryotes.

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15
Q

Which are the steps of initiation of transcription in prokaryotes?

A

1) Sigma binds to core complex
2) sigma of the Esigma complex scans the DNA and locates a promoter to which it binds, forming a closed initiation complex.
3) E.sigma then undergoes Temperature dependent conformational change and melts the nucleotides at the TTS (+1) and becomes PIC.
- unwinding allows the Esigma complex
4) RNAP catalyses the first two nucleotides and the chain is attached to the beta subunit of the holoenzyme.

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16
Q

Define the initiation reaction

A

Formation of the first phosphodiester bond. Linking the first 2 nucleotides.

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17
Q

What happens when about 10 nucleotides have been added to the transcribing rna chain?

A

Promotor clearance.

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18
Q

What is Promotor clearance?

A

When the RNAP has added about 10 nucleotides it will undergo conformational change and move away from the promoter. now elongation can begin.

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19
Q

what compound is released as a result of the catalysis of nucleotides during transcription and how does it differ from the same kind of event in DNA synthesis?

A

PPi is released.

In DNA synthesis this is broken down into two pi’s directly making the reaction irreversible.

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20
Q

How can both Pro and Eukaryotes regulate the transcription process by halting it?

A

Through decision to stay in the promotor site and not initiate elongation

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21
Q

What dictates the size of the transcription bubble?

A

Polymerase. it is however independent od the DNA sequence in the complex.

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22
Q

How is the DNA unwound during transcription in Prokaryotes?

A

By RNAP as well, since it has “intrinsic unwindase activity that opens up the helix.

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23
Q

How is the termination of transcription signaled in Prokaryotes?

A

Its signaled in the sequence of nucleotides in the template strand which is then recognised by the termination protein factor Rho P (p) factor

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24
Q

What is Rho?

A

An ATP dependent RNA stimulated Helicase that disrupts the ternary transcription elongation complex.

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25
Q

What is the ternary transcription elongation complex composed of?

A

DNA strand, RNA pol and hnRNA.

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26
Q

How can termination occur without Rho, in prokaryotes?

A

For some bacterial genes RNAP is able to directly recognise encoded termination signal sequences.

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27
Q

What is the role of RNAP II in eukaryotic transcription?

A

Catalyses the RNA chain. Enzymes catalysing RNA processing, Termination and and polyadenylation all seems to load onto the Pol II soon after initiation.

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28
Q

Simultaneous transcription

A

More than one polymerasse may transcribe the same template starnd of a gene at the same time, however each may only transcribe different portions of the strand.

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29
Q

What are promotors?

A

Regions to which RNAP can bind with high affinity. Promotor = TGTTGACA + prinbow/TATA-box
The two consensus sequences make up the promotor.

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30
Q

How is accurate transcription ensured?

A

Binding to promotor which has base specific association with the RNAP.

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31
Q

Define transcription unit.

A

promotor +following gene. eg. in bacteria lac operon is an example of a transcription unit.

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32
Q

Define structural gene.

A

also known as citron, the coding regions of the unit.

Each citron codes for one polypeptide chain.

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33
Q

Define Consensus sequence

A

A sequence in the promotor region that determine the affinity of RNAP to that area, thus determine the frequency of transcription.

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34
Q

How large is the promotor region?

A

approx 40 BP in total, thus whole can be covered by &) Bp large RNAP.

35
Q

When is the closed complex formed?

A 
When RNAP (or Esigma really) binds the consensus complex -35 upstream from the TSS.
this consensus sequence in Pro is TGTTGACA, about 8 nucleotides long.
36
Q

What is the Prinbow box?

A

The TATA box of the prokaryotes. its the consensus sequence located more proximal to the TSS (ca 10 nucleotides)

  • It is TA rich and where open coplex can be formed since melting is done more easily here.
  • its here where the Pol can access the template strand and form a
37
Q

What is the function of the sequences in between the two consensus sequences of the transcription unit?

A

critical spacing function that facilitates recognition of the two sites by RNAP.

38
Q

What can be found withing the Rho dependent termination signal sequences?
How does it effect the structure of the hnRNA?

A

Hypenated or interrupted consensus sequence reapeat of about 40 Bp followed by TAbp.
This causes the hairpin structure of the soon to be mRNA . when the transription passes through this sequence it will due to the repeats form the intramolecular hairpin structure as a result of H-bond base pairing and when it reaches the AT rich area it will with the help of Rho factor which stops the RNAP complex dissociate from the template strand.

39
Q

How does the initiation occur for the large number of eukaryotic genes that lack a TATA box?

A

RNA polymesase is directed to the promoter by an initiation sequence (Inr) and the downstream promoter element (DPE) to provide correct basal transcription.

40
Q

What is TFIID’s role in initiation of transcription in Eukaryotes?

A

Binds to the initiation sequence (Inr) to direct Pol 2.

41
Q

What is used for initiation of stronger or more transcribed genes?

A

Both TATA box and Inr sequence.

42
Q

the location of the consensus sequences of Eukaryotes VS prokaryotes?

A

Pro: -10 &-35

Eu -X & -25

43
Q

(E) which subunit of TFIID is bound to the DPE sequence?

A

TAF

44
Q

(E) How can the transcription frequency be dependent of the upstream sequences adjecent to the gene thats is going to be transcribed?

A

Mutations of these sequences can reduce transcription frequency with about 10-20 fold
Why u wonder, well i dont fucking know.

45
Q

(E) Which specific protein binds to the GC box?

A

Sp1, through its DNA binding domain.

46
Q

(E) Which specific protein binds to the CAAT box?

A

CTF, through its DNA binding domain.

47
Q

(E) What can regulate the freqency of regulation besides consensus sequences?

A

Protein protein interactions and activation domain interactions ??? kolla upp svaret lite vagt!

48
Q

What are enhancers?

A

positive regulators.

49
Q

(E) Where can enhancers and repressors be found?

A

Both down and upstream from the TSS and sometimes within the gene.
They can be located thousands of nucleotides away.

(they can function in a direction independent fashion) doent belong here but fun to know.

50
Q

(E) How constrained are these enhancers and repressors?

A

Very few are as constrained that the only allow the binding of a single protein, the majority of them allows several different proteins to bind.

51
Q

How can transcription be initiated if the promotor or enhancer is covered by nucleosomes?

A

Covered gene is inactive because of its inaccessibility of TATA and/or the DPE. Activation can be done through covalent histone modifications and co-regulators.

Complex has to be formed between the ATP-dependent chromatin remodellers and chromatin modifying co-regulators.

52
Q

How can the Histone co-regulator complexes “free the transcription needed site (TATA/Enhancer)?

A

1) through removal nucleotides or change in histones by octameric ATP dependent remodellers.
2) Covalent modification of the nucleosomal histones using intrinsic acetylases.

53
Q

How do the two promotor proximal signals control Eukaryotic transcription?

A

1) ……. Defines where transcription os to commence

2) …….Contributes frequency control of transcription

54
Q

which protein binds to the human TATA box?

A

TATA-binding protein (TBP)

55
Q

(E) Which complexes is TBP a subunit of?

A
  • TFIID (contains TBP-associated factor)

- SAGA/PCAF

56
Q

(E) What is TAF?

A

A non-TATA-binding protein subunit of TFIID

57
Q

(E) What is the CTD?

A

kk

58
Q

What indicates the first step of formation of transcription complex in eukaryotes?

A

The binding of the TBP-TAF-TFIID complex to the TATA box sequence.

59
Q

(E) How many steps can the transcription cycle be described in?

A

6

60
Q

(E) What’s the first step in the transcription cycle?

A

Binding and formation of Closed RNA Pol-promoter complex. (location of promoter site)

61
Q

(E) Whats the second step of transcription cycle?

A

PIC formation: open promoter complex formation.

62
Q

(E) What’s the third step in the transcription cycle?

A

Chain initiation: RNA polymerase catalyses the coupling of the first two bases. the first one is usually a purine.
-> dinucleotide formed.

63
Q

(E) What’s the 4th step in the transcription cycle?

A

Promotor clearance: When RNAP reaches a lenght if 10-20 nucleotides it undergoes a conformational change and is able to move away from the promoter and start transcribing the RNA.

64
Q

(E) What’s the 5th step in the transcription cycle?

A

Chain elongation: Catalysis, nucleophilic attack. same complex.

65
Q

(E) What’s the 6th step in the transcription cycle?

A

Termination: when termination sequence it undegoes additional conformational change which causes the RNAP to release the strand.

66
Q

what are all steps in eukaryotic transcription facilitated by?

A

pos and/or neg. -acting factors.

67
Q

what is a transcription unit?

A

The region that induces the signal for initiation of transcription.

68
Q

what number is the TSS designated if its located upstream from the transcription gene?

A

-1, and the numbering will be negative.In this case transcription is considered proceeding away from the TSS.

69
Q

what number is the TSS designated if its located downstream from the transcription gene?

A

+1, and the numpering will increasing/ positive.

70
Q

What RNA does pol II in eukaryotes transcribe?

A

mRNA precursor, hn RNA

71
Q

Why is the Cap necessary mRNA?

A

for processing of primary transcript, for the translation process and for protection from nucleolytic attack by 5’-Exonucleoases.

72
Q

Which gene is DNA-dependent Polymerase I and polII responsible for transcribing in eukaryotes, respectively?

A

kolla upp

73
Q

How many subunits does RNA pol III have

A

14

74
Q

which are the two large subunits that all 3 RNA polymerases have in eukaryotes?

A

……. the have strong structural and functional similarities to beta and beta prime subunits of Prokaryotic RNAP.

75
Q

How can alpha Aminitin inhibit trascription in eukaryotes?

A

It can block the RNA pol(2??) during phosphodiester bond formation.

76
Q

What does the mRNA 3’end formation depend on?

A

The CTD of the Largest subunit of RNA Pol II.

77
Q

Why does all the RNA polymerases in Eukaryotes need GTF’s?

A

Because they cant themself distinguish between the promoter sequences and other sequences of the dna.

78
Q

What has the role of sigma of prokaryotic transcription in Eukaryotic transcription?

A

TFII-A,BDEF&H are needed to promote the transcription by Pol II.

79
Q

What is TFIID composed of?

A

14 TAF’s and a TBP

80
Q

whats the role of TFIID?

A

It binds to the TATA box of the promoter through its TBP subunit , which is the only part of it that is independently able to bind to the promoter, to the minor groove. (Most other transcription factors bind to the Major groove)
The binding to the minor groove causes a 100 degree bend which facilitates the binding of other TBP-associated factors with other components of the transcription initiation complex.
The binding of TFIID marks the promotor for transcription.

81
Q

In which sequence does the GTF’s bing?

A

TFIID first binds to the promoter then TFIIA binds the the TFIIDF-Promoter complex and the TFIIB joins the party.
When these are all bound, the TFIIF complex which is already bound to Pol II binds to the complex, both complexes form one big.
After that TFIIH binds and pic is complete.

82
Q

What is formed when all GTF and pol II have bound to the promoter?

A

the complex becomes big enough to cover from -30 to +30 around the TSS.

83
Q

Which transcription factors are required for the genes that lack tata box?

A

The same as with tata box, only that Inr and/or DPE first have to position the complex.

84
Q

Where are the termination signals located in Eukaryotes?

A

Way downstream from the coding gene.

Biochem K (10 decks)

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