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Molecular Biology > Transcription and Translation 1 (lecture 7) > Flashcards

Transcription and Translation 1 (lecture 7) Flashcards

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1
Q

What are the major differences between DNA and RNA

A
  • RNA is single stranded
  • RNA has ribonucleotides instead of deoxyribonucleotides
  • RNA has Uracil instead of Thymine
  • RNA can fold into complex 3-dimensional structures allowing some RNAs to have precise structural and catalytic functions
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2
Q

Function of snRNAs

A

function in a variety of nuclear processes, including the splicing of pre-mRNA

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3
Q

function of snoRNAS

A

small nucleolar RNAs, help to process and chemically modify rRNAs

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4
Q

function of miRNAs

A

Micro RNAs, regulate gene expression by blocking translation of specific mRNAs and cause their degradation

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5
Q

Function of siRNAs

A

small interfering RNAs, turn off gene expression by directing the degradation of selective mRNAs and the establishment of compact chromatin structures

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6
Q

mRNA make up _____% of total cellular RNA

A

3-5%

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7
Q

do many genes have RNA as their final product

A

yes

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8
Q

non-coding RNA serve as ____ and ____ components for many biological processes

A

enzymatic and structural

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9
Q

Direct the splicing of pre-mRNA to form mRNA

A

snRNA

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10
Q

regulate eukaryotic gene expression by degrading select mRNA

A

small interfering RNA (siRNA)

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11
Q

Regulate gene expression by blocking translation of selective mRNA

A

micro RNA (miRNA)

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12
Q

Characteristics of prokaryotic RNA polymerase

A
  • Bacterial RNA polymerase (RNA Polymerase)- multi subunit complex
  • The holoenzyme is alpha2betabeta’sigma
  • Catalyzes the formation of phosphodiester bonds that link nucleotides
  • RNA polymerase has proof-reading nuclease activity
  • Lower fidelity of RNA synthesis can be tolerate
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13
Q

RNA transcription uses what strand

A

Template strand

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14
Q

what is the most important and most regulated step in gene expression

A

Initiation

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15
Q

The sigma subunit binds to the promotor to form an

A

open promoter complex

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16
Q

RNA polymerase assembles into holoenzyme _______

A

alpha2betabeta’sigma

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17
Q

sigma subunit binds to the promotor and unwinds a short ___BP segment of double stranded DNA to form a transcription bubble

A

17

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18
Q

When transcription begins a short RNA is formed via a_____ mechanism. The stress that is caused with polymerase still bound to promoter pulls DNA into active site causes short RNA to

A

scrunching mechanism, be released by abortive initiation

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19
Q

_____ of nucleoside triphosphate provides energy to form phosphodiester bonds and drive RNA polymerase forward

A

Hydrolysis

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20
Q

in prokaryotes two common promoter motifs are known as the ____ sequence and the ________ are present on 5’ upstream side of the transcription start site

A

-35 sequence (TTGACA) -10 sequence (TATAAT)

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21
Q

the sigma factor is released during what and reattached when

A

Sigma is released after promoter clearance, right before elongation. It is then reattached after termination

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22
Q

Elongation phase begins after the formation of

A

nascent RAN with about 10 nucleotides

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23
Q

Elongation generates superhelical tension that is eased by

A

DNA gyrase

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24
Q

Transcription continues till RNA polymerase meets

A

termination signals

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25
Q

Termination signals

A
  • Palindromic GC rich region followed by AT rich region
  • RNA transcript of this region is self complementary
  • forms a stable hairpin structure with a stem and a loop (due to high GC content)
  • This sequence followed by a poly(U) tail
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26
Q

what happens when RNA polymerase encounters stable hairpin loop

A
  • RNA polymerase pauses when it encounters this loop and formation of phosphodiester bonds stops
  • DNA-RNA hybrid destabilized due to rU-dA bonds (weak) and dissociates
  • Hairpin structure destabilizes the interaction of RNA with RNA polymerase and RNA dissociates
  • Unwound Region of DNA rewinds with its partner to form DNA duplex
  • Transcription bubble closes
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27
Q

In prokaryotes, all RNA molecules are synthesized by a single RNA polymerase while in eukaryotes there are ____ RNA polymerases.

A

3

28
Q

What RNA polymerase transcribes all protein-coding gens, plus snoRNA gens, miRNA genes, siRNA genes, INCRNA genes, and most snRNA genes in eukaryotes

A

RNA polymerase II

29
Q

What RNA polymerase transcribes tRNA genes, 5S rRNA genes, some snRNA genes, and genes for other small RNAs

A

RNA polymerase III

30
Q

Eukaryotic RNA polymerase II requires additional proteins during transcription these are known as

A

general transcription factors

31
Q

What are the unique features of RNA polymerase II

A
  • RNA polymerase II contains a unique carboxyl-terminal domain of the 220-kD subunit called CTD
  • The activity of RNA polymerase II is regulated by phosphorylation mainly on Ser residues of the CTD
32
Q

The general transcription factors for RNA polymerase II are denoted as

A

TFIIA, TFIIB,TFIIC, TFIID

33
Q

The general transcription factors for RNA polymerase II assemble at the _____ before ___

A

at the promoter before transcription

34
Q

Functions of general transcription factors for RNA polymerase II

A
  • help to position the RNA polymerase correctly at the promoter
  • Aid in pulling apart the two strands of DNA to allow transcription to begin
  • release RNA polymerase from the promoter into the elongation mode once transcription has begun
35
Q

Eukaryotic transcription begins with binding of ____ to the _____

A

TFIID to the TATA box

36
Q

what is the subunit of TFIID that recognizes TATA called

A

TATA-box binding protein (TBP)

37
Q

After TFIID is bound to TATA box ____ is recruited. Followed by ___, ____, ____ and ____. When all of these factors are joined they form the _____

A

TFIIB, TFIIF, RNA Polymerase II, TFIIE, and TFIIH, Transcription initiation complex

38
Q

What transcription factor is directly on RNA polymerase II

A

TFIIF

39
Q

what part of the transcription initiation complex unwinds the DNA double helix and exposes the DNA template strand.

A

TFIIH

40
Q

_________ of _____ by _____, causes RNA polymerase II to leave the promoter and begin elongation

A

phosphorylation of CTD by TFIIH

41
Q

what are the subunits of TFIID and their functions

A
  • TBP: recognizes TATA box

- TAF: Recognizes other DNA sequences near the transcription start point; regulates DNA-binding by TBP

42
Q

Function of TFIIB

A

Recognizes BRE element in promoters; accurately positions RNA polymerase at the start site of transcription

43
Q

Function of TFIIF

A

Stabilizes RNA polymerase interaction with TBP and TFIIB; helps attract TFIIE and TFIIH

44
Q

Function of TFIIE

A

Attracts and regulates TFIIH

45
Q

Function of TFIIH

A

Unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA polymerase CTD; releases RNA polymerase from the promoter

46
Q

____ box is the most common promoter sequence but some additional regualtory sequences are

A

TATA box, CAAT box, or GC box

47
Q

RNA polymerase II creates a superhelical tension as it moves along the eukaryotic DNA but this tension is removed by

A

DNA topoisomerase

48
Q

For a DNA molecule with one free end 0r a nick in one strand that serves as a swivel the DNA double helix rates by one turn every ____ nucleotide pairs opened. Since DNA helix does not have a free end it relieves the superhelical tension by bending into 1 ______ every ____ nucleotide pairs opened

A

10, supercoiled loops every 10 nucleotide pairs opened

49
Q

What is the difference between positive and negative supercoiling

A

Negative supercoils have the opposite handedness form the positive supercoils that form when a region of DNA helix opens. (note whenever a region of the helix opens it removes these negative supercoils from bacterial DNA, reducing the superhelical tension)

50
Q

Eukaryotic DNA i packaged into ______, which are arranged in higher order chromatin structures

A

Nucleosomes

51
Q

_____, a protein complex, allows the activator proteins to communicate with RNA Polymerase II and the general transcription factors

A

Mediator

52
Q

Chromatin modifying enzymes are recruited to provide greater access to DNA

A
  • Chromatin remodeling complexes

- Histone modifying enzymes

53
Q

Transcription elongation in eukaryotes is tightly coupled to ____ processing

A

RNA

54
Q

Immediate product of RNA polymerase II is _____ or ____

A

pre-mRNA or primary transcript

55
Q

Eukaryotic mRNA needs to be _____

A

processed

56
Q

____ modifications to mRNA are introduced to allow the cell to assess whether both ends of an mRNA molecule are present (message is intact) before it is exported form the nucleus to cytosol for translation

A

Covalent Modifications

57
Q

How is the RNA processed before translation in eukaryotes

A
  • Modification of the 5’ end of mRNA (RNA capping)
  • Removal of non-coding sequences (RNA splicing)
  • Modification of the 3’ end of mRNA (polyadenylation)
58
Q

The ___ end of the nascent RNA molecule is modified by addition of a cap

A

5’ end

59
Q

what is the structure of the 5’ RNA cap

A

7-methylguanosine joined to the 5’ end of RNA via a 5’-5’ triphosphate bridge.

60
Q

What is the role of the 5’ RNA cap

A
  • Helps to distinguish mRNA from other RNAs
  • Define The translation start site
  • Stabilizes mRNA by protecting their 5’ ends form phosphates and nucleases
  • Binds a protein complex CBC (Cap binding complex)- helps in RNA processing and export
61
Q

Eukaryotic genes are discontinuous because they are composed of ___ and ___

A

exons and introns

62
Q

The _____ must be excised and _____ linked to form the final mRNA (this process is called ____)

A

introns, exons, splicing

63
Q

mRNA splicing is carried out by _____ (assemblies of protein and small nuclear RNA)

A

Spliceosomes

64
Q

explain polyadenylation of 3’ end of pre-mRNA

A
  • The 3’ end of an mRNA is specified by a signal in DNA
  • This signal is transcribed into mRNA
  • These unique consensus sequences are AAUAAA, GU or U rich sequences and CA
  • recognized by RNA binding proteins and RNA processing enzymes
  • Two of the multisubunit proteins, called CstF (cleavage stimulation factor) and CPSF (cleavage and polyadenylation specificity factor) are of special importance
  • the two proteins travel the RNA polymerase tail and are transferred to the 3’ end processing sequence on the RNA molecule as it emerges from the RNA polymerase
  • The AAUAAA at 3’ end of RNA is bound by cleavage and polyadenylation factor (CPSF)
  • The GU rich element beyond the cleavage site is bound by cleavage stimulation factor (CstF)
  • CA sequence bound by a third factor
  • RNA is cleaved at the CA sequence by endonuclease
  • poly A polymerase (PAP) adds 200 A nucleotides to the 3’ end produced by the cleavage (from ATP) (note PAP does not require a template)
  • poly a binding proteins assemble onto the poly-a tail
65
Q

Bacterial mRNAs are ____, whereas eukaryotic mRNAs are mostly _____

A

polycistronic, monocistronic

66
Q

The 5’ and 3’ ends of bacterial mRNAs are not _____ while eukaryotic mRNA

A

modified, has a 5’ cap and a 3’ poly A tail

67
Q

Do bacterial mRNAs have introns

A

no ( but eukaryotes due so they must be removed by splicing)

Molecular Biology (14 decks)

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