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Biochemistry I > Transcription I > Flashcards

Transcription I Flashcards

1
Q

What are the differences btw RNA and DNA?

A

RNA

  • D-ribose instead of 2’-deoxyribose
    → can be hydrolyzed by alkalis to 2’, 3’ cyclic diesters due to presence of 2’-OH group
  • uracil instead of thymine
  • usually single strand instead of double strand (except in certain viruses)
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2
Q

List different types of RNA.

A

protein coding RNAs

  • mRNA: templates for protein synthesis

nonprotein coding RNAs

  • rRNA: form ribosomes
  • tRNA: adapter molecules for translation
  • small RNA: see own card
  • ribozymes: catalyticly active
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3
Q

List different types of small RNA.

A
  • snRNA
  • snoRNA
  • miRNA
  • siRNA
  • piwiRNA
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4
Q

What is snRNA?

Where can it be found + function?

A

small nuclear RNA

  • in eukaryotes, archae
  • involved in splicing of pre-mRNA
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5
Q

What is snoRNA?

Where can it be found + function?

A

small nucleolar RNA

  • in eukaryotes, archae
  • involved in chemical modification of rRNA/tRNA/snRNA
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6
Q

What is miRNA?

Where can it be found + function?

A

micro RNA

  • in eukaryotes
  • inhibition of translation of mRNAs
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7
Q

What is siRNA?

Where can it be found + function?

A

small interfering/silencing RNA

  • in eukaryotes
  • cause degradation of RNA molecules due to hybridization (= silencing)
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8
Q

What is piwiRNA?

Where can it be found + function?

A

Piwi-interacting RNA

  • in animals
  • protection against transposons
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9
Q

What are differences btw RNA and DNA synthesis, hence transcription and DNA replication?

A

in RNA synthesis

  • ribonucleotides used
  • U instead of T
  • no primer necessary, initiation starts de novo
  • only portions transcribed, genes can overlap to code for different proteins
  • no proofreading → lower fidelity
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10
Q

Differentiate btw coding, non-coding, and template strand.

A
  • template strand: DNA strand that is transcribed
    = non-coding/antisense strand
  • coding strand: DNA strand strand which has the same base sequence as the RNA transcript produced (obv T instead of U)
    = non-template/sense strand

​​NOTE: both strands can be used as templates though

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11
Q

What is asymmetric transcription?

A

both DNA strands could be used as templates, but transcription would be happening in opposite directions (still both in 5’→3’ direction)

just like DNA replication: synthesized in 5’→3’ direction, template read in 3’→5’

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12
Q

Describe the basic mechanism of transcription.

A
  1. requires the unwinding of the double helix at gene that should be transcribed
  2. RNA polymerase
    • catalyzes the formation of phosphodiester bonds between nucleotides
    • moves stepwise along the DNA extending the RNA chain as it goes
    • as it moves it unwinds the next part of the helix
  3. helix behind RNA polymerase closes and the mRNA is displaced
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13
Q

What are different features of DNA/RNA polymerase?

A

RNA polymerase

  • has intrinsic helicase activity
  • only works on one strand
  • does not require priming
  • does not proofread
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14
Q

How many types of RNA polymerase (RNAP) are there in prokaryotes?

Describe its structure.

A

only one type

4 subunits:

  • 2α: bind regulatory sequences
  • β: forms phosphodiester bond
  • β’: binds DNA template and σ factors
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15
Q

What are σ (sigma) factors, what do they do?

A

DNA-binding proteins, bind to β’ of prokarytoic RNAP to form RNAP holoenzyme Eσ

⇒ allow recognition of promoter

NOTE: σ factor considered an own subunit, so 5 subunits now

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16
Q

Describe the molecular mechanism how RNAP holoenzyme Eσ binds to the DNA.

A

recognizes atomic pattern in major groove of DNA (depending on base pairing)

  • acts as H donor, or acceptor, forming H-bridges
  • recognizes methyl groups, hydrophobic interactions
  • recognizes H atom, unavailable for H-bonding
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17
Q

What does the +/- numbering system indicate?

A
    • = upstream
    • = downstream

​ ⇒ way of defining the location of regulatory elements in a gene

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18
Q

How do you call the site on the DNA template where RNAP holoenzyme Eσ binds?

Structure.

A

promoter, upstream of transcription start site TSS

  • -35 region w/ consensus sequence TTGACA
  • 16-19bp spacer
  • -10 region, Pribnow box
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19
Q

What is the Pribnow box?

A

AT-rich sequence in prokaryotic promoters, easier unwinding due to only 2 H-bonds

→ similar to TATA box in eukaryotes

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20
Q

Differentiate btw types of σ factors.

A

​recognize different promoters + activate transcription of different genes

  • sigma 70: housekeeping sigma factor (normal one)
  • sigma 54: nitrogen-limitation sigma factor
  • sigma 38: starvation phase sigma factor, activates gene involved in long term survival (i.e. peroxisomes)
  • sigma 32: heat shock sigma factor

NOTE: variety of σ factors + competition for RNAP determines much of cell’s protein content

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21
Q

Which method is used to search for promoters on DNA?

A

footprinting

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22
Q

What happens after RNAP holoenzyme binds to the promoter?

A

forms pre-initiation complex
RNAP uses helicase activity to unwind dsDNA at Pribnow box, forming an open promoter complex

⇒ initiates transcription of new 5’ terminal of RNA a bit more downstrean at TSS (transcription start site)

23
Q

How is the first bond of the new mRNA during initiation of transcription formed?

A

standard mechanism
RNAP couples first base to second, formation of dinucleotide w/ phosphodiester bond

REMEMBER: strand synthesized in 5’→3’,
hence DNA template strand read in 3’→5’ direction

24
Q

Describe the elongation of prokaryotic transcription.

A
  1. after 8-9 bp of RNA synthesis, σ factor released
    = promotor clearance
  2. RNAP completes transcription at 30-50bp/s
    • unwinds (pos. supercoils of DNA) + reanneals behind enzyme (forming neg. supercoils)

⇒ RNA-DNA hybrid formed, but most RNA displaced as DNA helix reforms

25
What are the 2 types of termination of transcription? Differentiate btw pro- and eukaryotic termination.
(type I) **ρ-independent:**​ * in prokaryotes * _palindromic sequence_ forms a hair pin loop, destabilizes DNA-RNA hybrid (type II) **ρ-dependent:​** * in eukaryotes * termination protein _ρ factor_ binds to RNA, breaks H-bonds btw template DNA and RNA, then dissociates → disrupt elongation complex
26
How is the prokaryotic rRNA formed?
1. synthesized like mRNA. different precursor rRNAs are synthesized 2. 30S precursor rRNA cleaved by **RNase** to _16S rRNA, 5S rRNA_ (small ribosomal subunit), _23S rRNA_ (large ribosomal subunit) and selected _tRNAs_ _​​NOTE:_ precursor determines which tRNAs are produced
27
What do Svedberg units correspond to?
= **[S]** molecular size and shape
28
What does actinomycin D do? Which compound has a similar effect?
**acridine** * _intercalate btw successive G=C base pairs_ in dsDNA * inhibit transcriptional elongation _in pro- and eukaryotes_
29
What does rifampicin do?
_antibiotic_ * binds the β subunit of _bacterial RNA polymerase_ * blocks promoter clearance (elongation)
30
What are true activation and antirepression? Where does it occur?
occurs in eukaryotes to activate chromatin for transcription 1. DNA in _inactive ground state_ (condensed heterochromatin) 2. **antirepression:** conversion to _depressed state_ (deconsed euchromatin) 3. **true activation:** conversion to _activated state_
31
Describe the mechanism of activation of chromatin for transcription.
1. **transcription factor** binds to DNA + recruits histone acetylase (HAT) 2. **histone acetylase** acetylates histones to decr. interactions w/ DNA (ex: _H3 lysine9 acetylation_) 3. **chromatin remodeling complex** unwraps nucleosomes at the promoter in an _ATP-dependent manner_ _​_⇒ eventually RNAP holoenzyme bind to initiate transcription
32
How is transcription regulated in eukaryotes?
binding of **trans-acting factors** to **cis-acting elements** on DNA ⇒ controls transcription (= gene expression)
33
What are cis-acting elements? Examples.
_DNA sequences_ close to a specific gene, affecting its transcription * **promotors**: containing transcription start site * **enhancers:** regulatory DNA sequences, bind TFs to upregulate transcription * **silencers:** regulatory DNA sequences, reduce/shut off expression of a gene * **terminators:** stop signal for transcription
34
What are the characteristics of enhancers?
35
What are trans-acting factors? Examples.
usually proteins (can be hormones, heavy metals) that **bind to cis-acting elements** to _control gene expression_ * may be expressed in a spec. tissue * may be expressed at spec. time in development * may be required for protein mod. * may be activated by ligand binding ⇒ **RNA polymerases, transcription factors**
36
What are the 2 groups of transcription factors? Why are they important?
**specific + general TFs** * Pol I, Pol III promoters mainly require _general TFs_ * Pol II promoters mainly require _specific TFs_
37
How do transcription factors bind to cis-acting elements on DNA?
via **DBD** (_DNA binding domain_) → bind through H-bonds/van der Waals interactions to DNA in _major groove_ * **Zinc finger domain** * **helix-turn-helix domain** * **Leucine zipper domain** * **basic helix-loop-helix**
38
Differentiate btw eukaryotic RNAPs and their function. Where are they located?
_3 nuclear RNAPs:_ Pol I in nucleolus, others in nucleoplasm * **Pol I:** transcribes genes coding for _18S, 5.8S, 28S rRNA_ * **Pol II:** transcribes genes coding for _mRNA_, _miRNA, snRNA_ * **Pol III:** transcribe genes coding for _tRNA, 5S rRNA_ + **1 mitochondrial RNAP IV** ⇒ require _transcription factors_ to assemble at promoter
39
How are eukaryotic RNAPs structurally different from prokaryotic RNAP?
_additional subunits_ to provide **interaction sites for transcription factors, DNA and RNA**, and modulate diverse RNAP activities
40
What does α-amanitin do?
_in *Amanita phalloides* (death cap mushroom)_ **_potent_ inhibitor of RNA pol II** and **_weak_ inhibitor of RNA pol III** _NOTE:_ RNAP I = _insensitive_ to α-amanitin
41
How is mtDNA transcribed to mRNA?
**_both_** strands are transcribed (_entirely_) 1. _D loop contains promoter_ for each strand 2. RNA then cut into inidividual RNAs for each gene 3. protein-coding genes are poly-A-tailed, r/mRNAs modified as necessary
42
Explain the initiation of transcription at RNA Pol I promotors.
1. **upstream binding factor** (_UBF_) (2 subunits) binds to _upstream core element_ (UCE) and the _core promoter element_ (CPE) → protein-protein interactions to bring both closer together 2. subsequent binding of **selectivity factor I** (4 subunits) → stabilizes structure, _RNA pol I_ binds UBF somewhat similar to sigma factor in prokaryotes
43
What is the product of transcription of RNA pol I? How is it processed?
_pre-rRNA transcript 45S_ ⇒ **methylated + cleaved** to mature 18S, 5.8S, 28S rRNA
44
How are snoRNAs transcribed?
* **some** synthesis by _RNA pol II_ (having snoRNA specific promoters) * **majority formed from introns** * from genes coding for proteins that are involved in _ribosome synthesis/translation_ * from genes coding for _non-functional mRNAs_
45
Explain the initiation of transcription at RNA Pol III promotors. What are its transcriptional products?
1. transcription factor **TFIIIC** binds to _A and B box_ on DNA 2. trimeric **TFIIIB** binds immediately upstream of TSS → _recruits RNA pol III_ ​⇒ synthesizes 5S rRNA and tRNA (as seperate precursor RNAs) _BUT:_ mechanism for 5S rRNA slightly different again, here TFIIIC somewhat similar function to sigmar factor in prokaryotes
46
How is the transcription of 5S rRNA by RNA pol III different fromt that of tRNA?
**TFIIIA** has to bind to _C box_, before TFIIIC binds to A and B box
47
How are tRNAs processed?
1. **RNase P and D** insert cuts in _primary transcript_ 2. **bases modified** and other minor modifications done to form _intermediate_ 3. **spliced** to _mature tRNA_
48
What is one of the most frequent naturally occuring post-transcriptionally modified bases in tRNA? Structure.
**pseudouridine**
49
Which DNA region is especially important for the initiation of mRNA transcription by RNA pol II? Why?
**TATA box** located 25 nucleotides upstream from transcription start site, _AT-rich sequence_ for easier unwinding (2 H-bonds) → recognized by C-terminal of **TBP** (_TATA-binding protein_) of **TFIID**
50
How is the initiation of transcription catalyzed by RNA pol II initiated, once TFIID has bound to the TATA box?
1. several other **TFs and RNA pol III** assemble at promoter 2. **TFIIH** (helicase) * _hydrolyses ATP_ to unwind DNA at TSS * _phosphorylates_ RNA pol II 3. phosphorylation induces **conformational change** of RNA pol II → _release of TFs, escapes from promotor + starts elongation_
51
At which site is RNA pol II phosphorylated during initiation?
at long C-terminal polypeptide tail, also called the **C-terminal domain** (_CTD_) _NOTE:_ after termination and pol II release **de**phosphorylated again
52
What is the function of topoisomerases during the process of transcription?
precede and follow RNA polymerase in transcription bubble → **relieve torsional stress**
53
How do you call the primary transcript of RNA pol II? Where is it synthesized and what happens to it?
**heteronuclear RNA** (_hnRNA_) or **pre-mRNA** synthesized _in nucleus_ ⇒ receives **modifications** to prepare it for translation

Biochemistry I (13 decks)

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