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Molecular Cell Biology > Transcription 1&2 (Week 5) > Flashcards

Transcription 1&2 (Week 5) Flashcards

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1
Q

What does the role of RNA entail?

A

RNAs play a vital role in using that information to produce proteins.

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2
Q

Is RNA a linear or double stranded?

A

Linear Polymer

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3
Q

Is RNA ribose or deoxyribose based?

A

Ribose

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4
Q

What base replaces thymine in RNA?

A

Uracil

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5
Q

How is RNA copied from DNA?

A

The sequence of the RNA molecule is the complement of the TEMPLATE strand (3’-5’ )
The sequence of the RNA molecule is the same as the CODING strand (5’-3’ )
T in DNA is replaced by U in RNA

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6
Q

Can both strands of DNA act as templates or only one?

A

Both

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7
Q

How is RNAs ability to adapt to a secondary structure Important?

A

The ability to form complex secondary structures is important for tRNAs and rRNAs

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8
Q

List the major types of RNA in prokaryotes?

A 
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)
Messenger RNA (mRNA)
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9
Q

List the principle types of RNA produced in cells and their function?

A

mRNA - code for proteins
rRNA - form the basic structure of the ribosome and catalyse protein synthesis
tRNA - central to protein synthesis as adaptors between mRNA and amino acids
snRNA (small nuclear RNA) - function in a variety of nuclear processes including the splicing of pre-mRNA
snoRNA (small nucleolar RNA) - helps to process and chemically modify rRNAs
miRNA (microRNA) - regulate gene expression by blocking translation of specific mRNA and cause their degradation
siRNA (small interfering RNA) - turn off gene expression by directing the degredation of selective mRNAs and the establishment of compact chromatin structures
piRNA (piwi-interacting RNA) - bind to piwi proteins and protect the germ line from transposable elements
lncRNA (long non-coding RNA) - many of which serve as a scaffolds; they regulate diverse cell processes, including X-Chromosome inactivation.

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10
Q

What do Prokaryotic RNA polymerases consist of?

A

Prokaryotic RNA polymerase has 5 subunits, 4 make up the core polymerase and 1, the sigma factor, is required for initiation

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11
Q

What signals the start of transcription in prokaryotes?

A

the consensus sequences (ideal promoter sequences) -35 and -10 signal the start of transcription

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12
Q

What does the Haloenzyme do, during initiation? (1)

A

Holoenzyme (core polymerase + sigma factor) assembles

and locates a promoter

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13
Q

How does the process of elongation occur?

A

As polymerase moves along the template, sigma factor loses contact with the promoter.

Sigma factor is released, freeing the polymerase to progress rapidly along the template (~ 50 bases/sec)

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14
Q

How does the process of termination occur?

A

Termination signal coded in the DNA causes the formation of a hairpin loop in the RNA. This destabilises the polymerase’s hold on the RNA.

The completed RNA is released by the polymerase. The cycle can now begin again.

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15
Q

What does RNA polymerase I consist of?

A

RNA polymerase I - 5.8S, 18S, and 28S rRNA genes

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16
Q

List the role that TFIID subunits play in transcription?

A

TBP (subunit); Recognises TATA box (1 subunit)
TAF (subunit); Recognises other DNA sequences near the transcription start point; regulates DNA binding by TBP (11 subunits)

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17
Q

How does the initiation of transcription occur in eukaryotic cells?

A

Tata binding protein(part of TFIID) binds to the TATA box.

Conformational change in the DNA allows binding of TFIIB

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18
Q

How does TATA binding change the topography of the DNA?

A

TBP binds to the TATA box and induces a bend in the DNA helix
This may serve as a “landmark” to attract the other general transcription factors

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19
Q

How is the initiation complex assembled?

A

With TFII B and D bound, the other general factors and RNA polymerase II can now assemble.

20
Q

How does transcription start then in eukaryotic cells?

A

TFIIH has both helicase activity to start unwinding the DNA and Kinase activity to Phosphorylate CTD

Phosphorylation of CTD releases the pol II from the promoter sequence to begin transcription
(c.f. release of sigma) .

21
Q

What other factors are required in the start of transcription in Eukaryotic cells?

A

Most polymerase II promoters also need activator proteins and mediator complexes for efficient transcription (long range interactions) proteins to re-model the chromatin and modify histones to give greater access to the DNA are also needed

22
Q

What happens as elongation occurs?

A

Pol II transcripts undergo 3 major processing events as elongation proceeds: capping; splicing and tailing.

Phosphorylation events on the CTD mediate these events

23
Q

What is Capping?

A

A phosphatase removes a phosphate
from the 5’ end of the RNA.

Next a guanyl transferase adds GMP in 5’ to 5’ (not the usual 5’-3’) linkage

Finally a methyl transferase adds a methyl group to the guanosine.

The cap identifies the RNA as an mRNA

24
Q

Is mRNA same as the genomic template?

A

Prokaryotic mRNA is colinear with the genome.

Eukaryotic mRNA is discontinuous with its genomic template – sequences must have been removed from the primary transcript (introns).

25
Q

What cleavage event does splicing incur?

A

The A at the branch site site attacks the 5’ splice site, cutting the RNA.
The 5’ end of the intron becomes covalently bound to the A
The free OH then reacts with the 5’ end of the next exon, releasing the intron as a lariat.

26
Q

How do mutations and splicing link?

A

Mutations can lead to incorrect splicing

27
Q

How does termination occur in eukaryotic cells?

A

Termination is a two step reaction – cleavage and polyadenylation
Mediated by binding of proteins to the P-CTD (cleavage and poly adenylation specificity factors CPSF and cleavage stimulation factor, CstF)

After cleavage poly A polymerase adds untemplated As, to which poly A binding protein then attaches.
The pol II continues along the template, but the RNA now emerging has no cap and is degraded, eventually causing the pol II to release from the template

28
Q

What is the correlation between consensus sequences and termination?

A

Consensus sequences can dictate termination

29
Q

What happens to the final product of RNA in eukaryotic cells?

A

The mature mRNA is now ready for export to the cytoplasm, where it will be translated.

30
Q

What is the link between transcription and ribosomal RNA?

A

3 of the 4 rRNAs are transcribed by RNA pol I, as a single precursor.
The precursor is chemically modified (2’ OH methylation, and isomerisation of U to pseudouracil
The precursor is cleaved into 18S, 5.8S and 28S rRNAs
5S is transcribed by RNA pol III

31
Q

What are the chemical modifications directed by?

A

Methylation of ribose and isomerisation of uracil are carried out by snoRNPs (small nucleolar)

The snoRNAs basepair with the sites that are to be modified

32
Q

Do tRNA undergo modifications?

A

tRNAs are transcribed by RNA pol III and undergo extensive processing including: removal of the intron by endonuclease and ligase; replacing 3’ UU with CCA by the CCA-adding enzyme; modification of riboses and bases. See translation lecture for more detail on tRNA structure

33
Q

What is the role of mRNA?

A

mRNAs convey the information to the cell

34
Q

What is the role of tRNA and rRNA?

A

tRNA and rRNAs (as part of ribosomes) decode a nucleotide sequence to produce a polypeptide sequence

35
Q

What do Eukaryotic polymerases consist of?

A

Eukaryotic RNA polymerase II (there are 3 different polymerases in euks) has 12 subunits

36
Q

What does the sigma factor do, during initiation? (2)

A

Sigma factor makes contacts with -35 and -10 signals

37
Q

What does the polymerase begin to do, in initiation? (3)

A

Polymerase begins to unwind the DNA double helix.

38
Q

What does polymerase then start to do in initiation? (4)

A

Polymerase starts transcribing

39
Q

What can occur if sigma factor is still in contact with the promoter? (5)

A

this process may stall – “abortive initiation”

40
Q

What does RNA polymerase II consist of?

A

RNA polymerase II - All protein coding genes, plus sno-RNA genes, miRNA genes, siRNA genes, and most snRNA genes

41
Q

What does RNA polymerase III?

A

RNA polymerase III - tRNA genes, 5S rRNA genes, some snRNA genes, and genes for other small RNAs

42
Q

What role does TFIIB play in transcription?

A

Recognises BRE element in promoters; accurately positions RNA polymerase at the start site of transcription (1 subunit)

43
Q

What role does TFIIF play in transcription?

A

Stabalises RNA polymerase interaction with TBP and TFIIB; helps attract TFIIE and TFIIH (3 subunit)

44
Q

What role does TFIIE play in transcription?

A

Attracts and regulates TFIIH (2 subunits)

45
Q

What role TFIIH play in transcription?

A

Unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA polymerase CTD; releases RNA polymerase from the promoter (9 subunits)

Molecular Cell Biology (18 decks)

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