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Molecular Final > Transcription in Eukaryotes > Flashcards

Transcription in Eukaryotes Flashcards

1
Q

What is the difference of mRNA in prokaryotes and eukaryotes in terms of transcription?

A

In prokaryotes transcriptiona nd translation occur at the same time with ribosomes loading mRNA as its made however in eukaryotes mRNA must be transported from the nucleus prior to translation

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2
Q

What is the difference on prokyarotic and eukaryotic RNAPs?

A

Prokaryotic have a single RNAP that can switch sigma factors to accommodate different needs.

Eukaryotes have 3 distinct RNAPs all int he nucleus and each one only transcribes specific sets of genes and each one recognizes a different promotor

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3
Q

Who demonstrated the presence of the three different RNAPs?

A

Roeder and Rutter

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4
Q

What is eukaryotic RNAP1?

A

It is most active at low ionic strength

stimulated equally by Mn and Mg

Nuclear location

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5
Q

What is RNAP 2?

A

Most active at high ionic strength

pronounced stimulation by Mn

nucleoplasmic location

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6
Q

What is RNAP 3?

A

Active over a broad range of ionic strength

stimulated by Mn

nucleoplasmic location

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7
Q

What is the precursor to mRNAs?

A

hnRNA-heterogeneous RNA

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8
Q

What is snRNA?

A

small nuclear RNA

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9
Q

What is the Sedimentation coefficient? function?

A

’s’ Svedberg unit and it gives information about how rapidly a particle moves through viscous medium in the presence of a centripetal force

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10
Q

Alpha-amanitin is from what organism and what was it used for?

A

It is from the mushroom genus AMANITA. It was used to help elucidate what types of RNA are transcribed by RNAP

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11
Q

What was the effect of low concentration compared to high concentration of alpha-amanitin on the RNA polymerases?

A

At low concentration the alpha-amanitin completely inhibited RNAP2 but did not have any effect on the RNAP1 or 3. AT higher concentration the alpha-amanitin also inhibited RNAP3

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12
Q

The Class I promoter is recognized by what RNAP?

A

RNAP I

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13
Q

WHat gene is the class I promotor associated with?

A

rRNA precursor gene

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14
Q

How does the sequence of Class I promoters vary among different species?

A

The sequence os Class I promoters varies from species to species

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15
Q

What is more variable the promoters recognized by RNAP I or RNAP II? Why?

A

The promoters recognized by RNAP I

RNAP II promoters tend to have more conserved elements

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16
Q

EVen though the sequence of the CLass I promoter is not well conserved what part of the Class I promoter is?

A

The general architecture

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17
Q

What is the structure of the CLass I promoter?

A

It consists of a core element located between -45 and +20 surrounding the transcription state site and an upstream control element (UCE) located between -156 and -107

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18
Q

WHat does the spacing between the core element and the upstream control element in the class I promoters determine?

A

The strength of the promoter

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19
Q

What can decrease the strength of the class I promoter?

A

Insertions or deletions between the core element and the upstream control element. The promoter is more sensitive to deletions.

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20
Q

What are Class II promoters recognized by?

A

RNAP II

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21
Q

What are the two major components of Class II promoters?

A
  1. Core promoter

2. Upstream element

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22
Q

What are the three parts of the core promoter of the class II promoter?

A
  1. Tata Box (~-30)
  2. Initiator (centered on the start site)
  3. Downstream element
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23
Q

What is the Tata box?

A

It is the most common element in class II promoters and has a consensus sequence of TATAAAA (nontemplate)

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24
Q

WHat other sequence is the Tata box similar to? and how is it different?

A

The -10 box in prokaryotes but its location is a greater distance from the transcription start site

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25
Q

What two groups of genes normally do not have tata boxes?

A
  1. housekeeping genes-genes that are always (constitutively) active and control common pathways
  2. developmentally regulated genes
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26
Q

WHat are specialized genes and do they contain tata boxes?

A

Specialized genes are luxury genes that code for proteins that are only made in certain cells such as keratin in skin cells and hemoglobin in red blood cells. They do contain Tata boxes

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27
Q

WHat is the general function of Tata boxes?

A

They help position the start of transcription

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28
Q

What are upstream elements also called?

A

GC boxes

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29
Q

What do upstream elements have and what do they do?

A

They have GC rich sequences that are located upstream from the tata box and serve to stimulate transcription

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30
Q

WHat type is element is the CCAAT Box?

A

upstream

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31
Q

What do the GC and CCAAT boxes require to be stimulatory?

A

The binding of transcription factors

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32
Q

What are initiators?

A

Conserved sequences found in some Class II Promotors. They are located around the transcription start site and are required form optimum transcription

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33
Q

Can transcription occur without the presence of initiators?

A

Yes but it is not optimum

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34
Q

Do initiators have a consensus sequence?

A

Yes

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35
Q

WHat are downstream elements?

A

They are sequences located downstream of the transcription start site. They are a fairly recent discovery and have not been fully characterized.

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36
Q

Do downstream elements have consensus sequences?

A

No

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37
Q

What are Class III promotors?

A

They are sequences recognized by RNAP III and they code for a variety of gnes that encode form small RNAs such as the 5s RNA and tRNA.

38
Q

What two genes are considered the “classical” CLass III genes? And where are their promoters located?

A

The genes that encode for the 5sRNA and the tRNA

Their promoters are located entirely within the genes

39
Q

What three parts is the internal promoter of the 5sRNA divided into?

A
  1. Box A
  2. Intermediate element
  3. Box C
40
Q

How was the importance of each of the promoter elements in the class III promoters determined?

A

By deletion experiments and site directed mutagenesis experiments. After the deletion or mutagenesis the altered gene was transcribed and the transcription efficiency was determined and compared with the unaltered gene.

41
Q

Where are the enhancers and silencers of transcription located?

A

promoter associated DNA but are not actually part of the promoter

42
Q

What is the function of enhancers and silencers? What do they need to be functional and what is the name of it?

A

They enhance or silence transcription when there are specific DNA binding proteins attached to them called transcription factors, enhancer binding proteins, activators?

43
Q

The specific DNA binding proteins that allow the enhancers and silencers to influence transcription are called what?

A

transcription factors
enhancer binding proteins
activators

44
Q

WHat are general transcription factors?

A

other DNA binding proteins that interact with the specific DNA binding proteins:transcription factors, enhancer binding proteins, activators to enable them to bind to DNA

45
Q

The Class II promotors the preinitiation complex contains what?

A

RNAP II and 6 general transcription factors

46
Q

what are the 6 general transcription factors in Class II promoters?

A 
TFIIA
TFIIB
TFIID
TFIIE
TFIIF
TFIIG
47
Q

How many general transcription factors are found in Class I promotors and what are they called?

A

2
SL1
UBP(upstream binding protein)

48
Q

How many general transcription factors are found in CLass III promotors and what are they called?

A

3
TFIIA
TFIIB
TFIIC

49
Q

What also influences transcription activity?

A

chromatin structure

50
Q

What does the presence of histone proteins (H2A H2B H3 H4) on DNA have on transcription? What type of influence on transcription is this?

A

It represses transcription by 75% versus naked DNA.

Chromatin structure

51
Q

What can be done when there is a presence of histones on DNA that is repressing transcription?

A

The acylation of histone loosens its association with DNA and will enhance transcription. Acylation is done throught the action of HAT (histone acetyl transferase)

52
Q

Most eukaryotic genes are interrupted by what?

A

Nonsense DNA

53
Q

Can RNAP tell the difference between coding regions and nonsense regions within the gene it is transcribing?

A

NO

54
Q

What is slicing?

A

The process of removing nonsense DNA from RNA transcripts followed by joining the coding regions together

55
Q

What are introns?

A

non coding regions of the transcript

56
Q

What are exons?

A

coding regions of the transcript

57
Q

What is a lariat?

A

Loop

58
Q

How are introns recognized?

A

The first two bases of an intron are nearly always GU and the last two bases are nearly always AG

59
Q

The slice sites have what kinds of sequences?

A

consensus sequences that extend past the GU and AG regions

60
Q

What is the three steps in the mechanism of splicing?

A
  1. The 2’OH group for the A residue within the intron reacts with the phosphodiester bond that links the first exon (exon 1) to the intron.
  2. A free exon 1 is released and the lariat intron-exon intermediate having the GU at the 5’-end of the intron in the phosphodiester linkage with the “reacting” A
  3. The free 3’-OH on exon 1 reacts with the phosphodiester bond between the intron and the exon 2. This produces the spliced exon 1 and exon 2 molecule plus the free lariat intron
61
Q

What is the “branch point A” in the splicing mechanism identified by?

A

The consensus sequence that surrounds it

62
Q

What is the “branchpoint A” sequence in yeast? How does this differ from the consensus sequence found in eukaryotes?

A

it is always the last A in the sequence UACUAAC

The sequence is more variable in eukaryotes- UNCURAC

63
Q

What are spliceosomes?

A

The 40s(yeast) or 60s(human) particle where splicing actually takes place.

64
Q

What is the spliceosome composed of?

A

lariat shaped splicing intermediate plus the particle

65
Q

Spliceosome formation depends on what and what is the spliceosome required for?

A

ATP dependent and it is required for efficient splicing

66
Q

What are SNURPS (snRNPs)?

A

small nuclear ribonucleoproteins

67
Q

What do What do snRNPs do?

A

Recognize the consensus sequence at the ends and brach points of introns and they assist in the bringing togetehr of the ends of consensus sequences to allow for splicing

68
Q

What do snRNPs consist of?

A

small nuclear RNAs coupled to proteins

69
Q

Approximetely how many pre-mRNAs in 20 total can be spliced in more than one way?

A

one

70
Q

Splicing a mRNA in more than one way leads to what?

A

that 2 or more alternate mature mRNAs can be made from the same transcript meaning 2 or more different proteins can be made from the same transcript

71
Q

Can RNA self splice?

A

yes some RNA can splice themselves without the help of a spliceosome or any protein participant

72
Q

What are self splicing RNAs known as?

A

“catalytic” RNA known as ribozymes

73
Q

WHat is the only known example of a non-protein molecule exhibiting enzyme characteristics ?

A

ribozyme

74
Q

WHat was the fist self splicing RNA discovered? WHere was it able to self splice?

A

Tetrahymena 265 r RNA precursor

in vitro

75
Q

__________ mRNA are methylated and a significant amount of the methylation is localized on the _______ of the mRNA.

A

Eukaryotic

5’-end

76
Q

What is capping?

A

The methylation of the 5’-end of the mRNA

77
Q

the extent of methylation can vary?

A

true

78
Q

What are the three types of methylation?

A

Cap 0
Cap 1
Cap2

79
Q

WHat is Cap 0 methylation?

A

It involves only the 7-methylguanosine at the 5’-end

80
Q

WHat is Cap 1 methylation?

A

It is the Cap 0 structure plus the next nucleotide with a 2’-O-methyl group

81
Q

What is the Cap 2 methylation?

A

The Cap 1 structure plus the 3rd nucleotide haveing a 2’-O-methyl group

82
Q

Draw the structures of the Cap 0,1,2 methlation

A

yes paper look

83
Q

CAPS have four major function what are they?

A
  1. They protect mRNAs from degradation
  2. They enhance the translatability of mRNAs
  3. Facilitate export from the nucleus to the cytoplasm
  4. They enhance the efficiency of splicing of mRNA
84
Q

how does capping allow the translatability of mRNAs to be enhanced?

A

It allows the mRNA to associate with ribosome via a cap binding protein

85
Q

How do caps protect mRNAs from degradation?

A

They have resistance of RNAse through triphosphate linkages

86
Q

What is the process of capping?

A

After receiving the mono methyl m7G cap in the nucleus RNA will migrate to the cytoplasm where it will form a snRNP and the cap becomes trimethylated then it reenters the nucleus for splicing and ultimate export back to the cytoplasm

87
Q

What is a precursor to mRNA?

A

hnRNA

88
Q

The ____ ends of hnRNA and mRNA possess a long chain of about 200-250 AMP residues. what is this called?

A

3’-ends

Poly A

89
Q

The poly A tail is made by transcription of a long series of Ts.

A

NOOOO it is added post transcriptionally in the nucleus by poly A polymerase

90
Q

What is the function of poly A?

A

It adds to the stability of the mRNA (ie protecting it from degradation) and it stimulates transcription

91
Q

What does Poly A binding protein I do?

A

It associates with polyadenylated mRNA and boosts translation efficiency

92
Q

There is evidence that some RNA is polyadenylated before splicing and some after splicing what does this mean?

A

The absence of poly A serves a signal for the destruction of the “de-polyadenylated” mRNA

Molecular Final (4 decks)

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