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SMP - Genetics > Lecture 5 - Transcription and RNA Processing > Flashcards

Lecture 5 - Transcription and RNA Processing Flashcards

1
Q

Do RNA polymerases require a primer?

A

NOPE

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2
Q

Does nascent RNA remain hybridized to template DNA?

A

NOPE

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3
Q

Which is more permanent: RNA or DNA?

A

DNA

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4
Q

Which is more accurate: replication or transcription?

A

Replication

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5
Q

How frequent are errors during transcription?

A

1 per 10,000 nucleotides

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6
Q

Are RNA and DNA polymerases structurally and evolutionarily related?

A

NOPE

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7
Q

Why do many errors during transcription go unnoticed?

A

Because many RNA strands are synthesized

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8
Q

What are mRNAs? Function?

A

Messenger RNAs

Code for proteins

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9
Q

What are rRNAs? 2 Functions?

A

Ribosomal RNAs

  1. Form the basic structure of the ribosome
  2. Catalyze protein synthesis
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10
Q

What are tRNAs? Function?

A

Transfer RNAs

Central to protein synthesis as adaptors between mRNA and AAs

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11
Q

What are snRNAs? Function?

A

Small nuclear RNAs

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

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12
Q

What are snoRNAs? Function?

A

Small nucleolar RNAs

Used to process and chemically modify rRNAs

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13
Q

What are scaRNAs? Function?

A

Small cajal RNAs

Used to modify snoRNAs and snRNAs

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14
Q

What are miRNAs? Function?

A

MicroRNAs

Regulate gene expression typically by blocking translation of selective mRNAs

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15
Q

What are siRNAs? Function?

A

Small interfering RNAs

Turn off gene expression by directing degradation of selective mRNAs and the establishment of compact chromatin structures

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16
Q

What is the function of other noncoding RNAs? 3 of them

A

Function in diverse cell processes like:

  1. Telomere synthesis
  2. X-chromosome inactivation
  3. Transport of proteins into the ER
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17
Q

How are different types of RNAs synthesized?

A

By different types of RNA polymerases

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18
Q

Are both DNA strands used as templates during transcription?

A

Not necessarily

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19
Q

How do we call the DNA strand that is not used as the template during transcription? 3 names

A

Nontemplate strand = coding strand = sense strand

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20
Q

In what direction is RNA synthesized during transcription?

A

5’ => 3’

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21
Q

How is the template strand assigned?

A

Functional assignment: called this only when it is serving as the template, which depends on the type of RNA polymerase used and what direction it moves in which is dependent on the direction of the gene

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22
Q

How to tell the direction of transcription?

A

As the RNA polymerase moves the RNA gets longer and longer

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23
Q

What is a transcription bubble?

A

Small strand separation in which the RNA polymerase reads the DNA template strand and synthesizes RNA

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24
Q

How is the nascent RNA released by the RNA polymerase?

A

Released from a ribosomal complex on the RNA polymerase

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25
Q

What are the 3 types of eukaryotic RNA polymerases and what types of RNA does each synthesize? Which ones accounts for most of RNA synthesis?

A

I: 5.8S, 18S, and 28S rRNAs (70% of RNA synthesis)
II: mRNA, snoRNA, and some snRNA
III: tRNA, 5S RNA, some snRNA (for splicing and poly(A)), scRNA (SRP = signal recognition peptide)

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26
Q

Which type of RNA is regulated more finely and precisely?

A

mRNA

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27
Q

What is another name for mRNA?

A

Pol II transcript

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28
Q

What are the 2 main differences between bacterial and eukaryotic RNA polymerases?

A
  1. Bacterial RNA pol requires only 1 single protein (sigma factor) for initiation, vs eukaryotic RNA pol require many additional proteins (general transcription factors)
  2. Eukaryotic transcriptional initiation must deal with the packaging of DNA in nucleosomes
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29
Q

Where is the promoter located? What are its 2 responsibilities? What does this mean for the sequences?

A

Sequence of DNA that is 5’ to the initiation site of the gene: the 5’ flanking region, which may also contain enhancers or other protein binding sites

Telling the RNA pol:

  1. Where transcription is going to start
  2. In what direction transcription should go

Therefore, the promoter is non-palindromic because DNA sequences that are non-palindromic are orientation-dependent and it is also position-dependent

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30
Q

What are the 3 regions of the promoter?

A
  1. Distal region
  2. Proximal region
  3. Core region
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31
Q

How is the promoter numbered?

A

Transcription starts at +1 so the promoter is negatively numbered

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32
Q

What is the role of the elements of the core promoter?

A

Binding sites for transcription factors associated with the initiation that create a large complex to create the right environment for RNA pol II to bind

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33
Q

What are the 4 elements of the core promoter? Positions? Do all core promoters contain all 4?

A
  1. BRE = B response element: -37 to -32
  2. TATA: -31 to -26
  3. Inr = initiator: -2 to +4
  4. DPE = downstream promoter element: +28 to +32

NOPE

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34
Q

What binds the TATA box?

A

A protein subunit of TFIID called the TATA binding protein (TBP)

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35
Q

What core promoter element is contained in ALL human neuropeptide promoter sequences?

A

TATA box

36
Q

What are the 3 elements of the proximal promoter?

A
  1. CCAAT box
  2. GC boxes
  3. CRE = cAMP response element
37
Q

What is the element of the distal promoter?

A

NRE = negative response element

38
Q

What are the 5 general transcriptional factors needed for initiation in eukaryotes?

A
  1. TFIID
  2. TFIIB
  3. TFIIF
  4. TFIIE
  5. TFIIH
39
Q

What are the 2 subunits of the general transcriptional factors needed for initiation TFIID and each of their function?

A
  1. 1 TBP subunit: recognizes TATA box
  2. 11 TAF subunits (TBP associated factors): recognizes other DNA sequences near the transcription start point and regulate DNA-binding by TBP
40
Q

2 roles of general transcriptional factors needed for initiation TFIIB?

A
  1. Recognizes BRE

2. Positions RNA Pol at the start site of transcription

41
Q

2 roles of general transcriptional factors needed for initiation TFIIF?

A
  1. Stabilizes RNA pol interaction with TBP and TFIIB

2. Helps attracts TFIIE and TFIIH

42
Q

Role of general transcriptional factors needed for initiation TFIIE?

A

Attracts and regulates TFIIH

43
Q

2 roles of general transcriptional factors needed for initiation TFIIH?

A
  1. Unwinds DNA at the transcription start point using ATP to create the transcription bubble
  2. Phosphorylates Ser5 of RNA Pol C-terminal domain (CTD) using ATP, which releases RNA Pol from other factors at the promoter
44
Q

Describe the 5 steps of transcription initiation.

A
  1. TBP of TFIID binds the TATA box
  2. TFIIB binds BRE
  3. TFIIE and TFIIH + TFIIF bound to RNA Pol II with other factors all bind to the DNA
  4. UTP, ATP, CTP, and GTP are all used for helicase activity of TFIIH and CTD phosphorylation
  5. Disassembly of most transcriptional factors
45
Q

Which 2 TAFs recognize and bind Inr?

A

TAF 1 and 2

46
Q

What is the role of the phosphorylation of the CTD by TFIIH?

A
  1. Release of RNA Pol from promoter region

2. Binding sites for further transcription factors: capping factors, splicing proteins, and 3’ end processing proteins

47
Q

What are 4 additional requirements of eukaryotic transcription initiation?

A
  1. Enhancer binding site for activator protein to regulate the expression rate of a gene
  2. Mediator (which is bound by the activator protein)
  3. Chromatin-remodeling complex
  4. Histone-modifying complex
48
Q

What is the role of the mediator in transcription initiation? Does it bind to DNA?

A

Coordinates all of the transcription factors throughout the promoter by binding to them with protein binding domains

NOPE

49
Q

What is the role of the chromatin remodeling complex in transcription initiation?

A

Remodels the chromatin to expose the DNA and make it available for a transcription bubble to be created

50
Q

How does transcription elongation affect the rest of the DNA?

A

It produces superhelical tension in DNA: the transcription bubble unwinds 10 DNA bps (1 helical turn) so the DNA helix forms supercoils if it has a fixed end or rotate 1 turn if it has a free end

In vivo it has fixed ends so it creates negative supercoiling behind the transcription bubble and positive supercoiling ahead of it

51
Q

How does negative supercoiling affect helix opening?

A

It facilitates it

52
Q

How does positive supercoiling affect helix opening?

A

It hinders it

53
Q

When does RNA processing occur?

A

Co-translational process

54
Q

What happens during splicing? Overall and 3 steps

A

Primary RNA transcript is processed to eliminate the introns that have been transcribed:

  1. Recognition of conserved sequences at intro/exon borders including conserved interior sequences
  2. Removal of intervening sequences with a lariat and 3’ end outside the loop
  3. Ligation of mRNA back together
55
Q

What are the 3 different RNA processing activities?

A
  1. 5’ capping
  2. Splicing
  3. 3’ polyadenylation
56
Q

Does RNA processing happen in prokaryotes? Why?

A

The 5’ capping and the 3’ polyadenylation happen but that’s it because they do not have DNA introns to excise and the mRNA does not have regulatory binding sites

57
Q

What is the purpose of the 5’ cap? 3

A
  1. Aids mRNA nuclear export
  2. Protects from 5‘ - 3‘ exonuclease degradation in cytoplasm
  3. Targets transcripts to ribosome for translation
58
Q

What is the purpose of the 3’ polyadenylation? 4

A
  1. Participates in termination of transcription
  2. Aids mRNA nuclear export
  3. Protects from 3‘ - 5‘ exonuclease degradation in cytoplasm
  4. Targets transcripts to ribosome for translation
59
Q

Are all regions of eukaryotic mRNA coding for a protein?

A

NOPE

60
Q

Are all regions of prokaryotic mRNA coding for a protein?

A

NOPE

61
Q

What is the main difference between prokaryotic and eukaryotic mRNA?

A

Prokaryotic mRNA products code for multiple proteins, eukaryotic mRNA products only code for 1 protein

62
Q

What is the half life of mRNA in bacteria?

A

~2 min

63
Q

What is the half life of mRNA in eukaryotes? What does it depend on?

A

min to 10 hrs: VERY variable

Depends on the presence of the 5’ cap and the length of the poly A tail

64
Q

Can the length of the poly A tail be regulated?

A

YESSSS

65
Q

Describe the process of adding the 5’ cap on eukaryotic mRNA.

A
  1. PPPNPNP-DNA = PPNPNP-5’DNA + Pi
  2. PPNPNP-5’DNA + GTP = GPPPNPNP-5’DNA + PPi (5’ => 5’ triphosphate bridge formation)
  3. GPPPNPNP-5’DNA + methyl group = CH3-(G+)-PPPNPNP-5’DNA
  4. CH3-(G+)-PPPNPNP-5’DNA + methyl group = CH3-(G+)-PPPN(-CH3)PNP-5’DNA (methyl is added to sugar on SOME caps)
66
Q

What is the full name of the 5’ cap?

A

7-methylguanosine triphosphate

67
Q

What is meant when we refer to RNA Pol II as an “RNA factory”?

A

During elongation it brings along all of the necessary components to generate a full length mRNA

68
Q

How was splicing discovered?

A

Took mature mRNA and back hybridized it to the DNA and saw that many regions of the DNA were not hybridizing with the mRNA and the looping parts were the introns

69
Q

What is alternative splicing?

A

Regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene.

70
Q

What is an example of alternative splicing?

A

Calcitonin gene can either produce calcitonin in the thyroid or CGRP (calcitonin gene related peptide) in the brain (involved in taste formation)

71
Q

What is RNA splicing conducted by?

A

The spliceosome, an snRNP (small nuclear ribonucleoprotein containing snRNA)

72
Q

What is the exon definition hypothesis?

A

Exons tend to be shorter than introns and thus simpler to define which is how splicing occurs and helps as splice junctions are not well conserved and therefore not that easy to identify

73
Q

How does the exon definition hypothesis describe splicing?

A
  1. SR proteins bind to each exon sequence in the pre-mRNA and thereby help to guide the snRNPs to the proper intron/exon boundaries.
  2. The intron sequences in the pre-mRNA, which can be extremely long, are packaged into hnRNP (heterogeneous nuclear ribonucleoprotein) complexes that compact them into more manageable structures and perhaps mask cryptic splice sites. It has been proposed that hnRNP proteins preferentially associate with intron sequences and that this preference also helps the spliceosome distinguish introns from exons. However, as shown, at least some hnRNP proteins may bind to exon sequences but their role, if any, in exon definition has yet to be established.
74
Q

What are SR proteins?

A

Proteins rich in Ser and Arg

75
Q

What happens during termination? 4 steps

A
  1. Consensus nucleotide sequence (AAUAAA) is recognized by CPSF (cleavage and polyadenylation stimulation factors) bound to 5’ side of cleavage site and CstF (cleavage stimulation factor) bound the rest of the 3’ sequence (GU or U rich)
  2. Cleavage at CA-OH and polyadenylation
  3. GU or U rich sequence is degraded in the nucleus
  4. Poly A polymerases adds the poly A tail
76
Q

What is the role of poly-A-binding proteins?

A

They stabilize the poly A tail

77
Q

What happens to the mature mRNA once it reaches the cytoplasm? What is the purpose of this?

A

It starts collecting all these proteins (including initiation factors for protein synthesis) that will recognize the 5’ cap and 3’ tail and will interact with each other to form a cyclic structure where the 5’ cap is bound to 3’ tail to ensure that the mRNA is intact

78
Q

What happens when you decap the mRNA?

A

Rapid 5’ to 3’ degradation

79
Q

What happens when you the remove the mRNA poly A tail?

A

Rapid 3’ to 5’ degradation

80
Q

What is an example of a cytoplasmic deadenylases? How does it work?

A

e.g. PARN binds the 5’ cap and starts chewing up the 3’ poly A tail leading to mRNA degradation

81
Q

What is more likely to happen to mRNAs with longer poly-A tails?

A

More likely to be translated

82
Q

How are all genes read?

A

3’ => 5’

83
Q

Where and when does binding of SR proteins to exons happen?

A

This demarcation occurs co-transcriptionally, beginning at the CBC (cap-binding complex) at the 5′ end.

84
Q

Describe the structures formed by introns packaged into hnRNPs.

A

Each hnRNP complex forms a particle approximately twice the diameter of a nucleosome, and the core is composed of a set of at least eight different proteins.

85
Q

What transcription factors bind Inr?

A

TAF 1 and 2 (subunits of TFIID)

86
Q

Is the 5’ flanking region transcribed into RNA?

A

NOPE

SMP - Genetics (16 decks)

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