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RNA metabolism Flashcards

1
Q

How does RNA differ from DNA

A

RNA has a hydroxyl group on carbon 2

Uracil but not thymine
Single stranded

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2
Q

RNA is both ___ and ___ (functions)

A

Genetic

Catalytic

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3
Q

Three major classes of RNA

A

mRNA
tRNA
rRNA

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4
Q

what is transcriptome

A

Collection of all transcripts in the cell

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5
Q

Three well understood rules of RNA

A

-Messenger RNA encode the amino acid sequences of all the polypeptides found in the cell

  • Transfering and matching aminoacids to triplets in mRNA
  • Ribosomoal RNA are the constituents of ribosomes
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6
Q

RNA can act as ____ in viruses

A

Genetic material

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7
Q

How do microRNA regulate the expression of genes?

A

Via binding to specific nucleotide sequence

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8
Q

Similarities between DNA replication and RNA synthesis

A
  • Addition of complementary nucleotide
  • Requirement of template
  • Direction of synthesis ( 5’ to 3’)
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9
Q

Differences between DNA replication and RNA synthesis

A
  • No primer required
  • Segment of DNA is used as template
  • One strand act as a template
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10
Q

RNA transcript is complementary to ____ and identical to ___

A

Complementary to DNA template strand

Identical to DNA nontemplate (coding) strand

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11
Q

Polymerase II reads the template strand strand in what direction

A

In 3’ to 5’

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12
Q

In what direction usually RNA transcript , DNA template strand and DNA coding strand are written

A

RNA transcript and DNA coding strand->5’ to 3’

DNA template strand ->3’ to 5’

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13
Q

How do nucleotide complement to each other

A

A purine are paired with pyrimidine , A+T->2 bonds

G+C-> 3 bonds

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14
Q

Pyrimidine is ___

Purine ___

A

Pyrimidine->2 rings(adenine, guanine)

Purines->2 ring (uracil,thymine,cytosine)

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15
Q

You always have ___ amount of purines and pyrimidines

A

Equal

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16
Q

In what form do nucleotides come

A

In triphosphate group

ribo-NTPs

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17
Q

There are three phosphates in NTPs: alpha, beta and gamma. What phosphate is connected to the sugar in the nucleotide

A

Alpha phosphate is connected to 5th carbon of the sugar ring

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18
Q

What is required for RNA synthesis

A

DNA template, all 4-ribo-NTPs and Mg

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19
Q

Explain how nucleotides are added to the growing RNA strand

A

The reaction involves two Mg2+ ions, coordinated to the phosphate groups of the incoming nucleoside
triphosphates (NTPs) and to three Asp residues, which are highly conserved in the RNA polymerases of all species. One
Mg2+ ion facilitates attack by the 3′-hydroxyl group on the α phosphate of the NTP; the other Mg2+ ion facilitates
displacement of the pyrophosphate. Both metal ions stabilize the pentacovalent transition state.

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20
Q

What domain of the polymerase has the site where the actual bonding between two nucleotides occur

A

Beta site

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21
Q

How does polymerase decide which DNA strand will be the template?

A

It can copy from any of the strand , but always it copies or “reads” in the direction of 3’ to 5’ and RNA will be from 5’ to 3’ direction

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22
Q

What is TSS

A

transcription start site (+1)- the first nucleotide that is transcribed into RNA

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23
Q

Similar looking sequences are classified as

A

Consensus sequences

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24
Q

Transcription cycle is also called

A

Sigma cycle

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25
Three main stages in sigma cycle
Initiation Elongation Termination
26
What are initial TFs that help to bind RNA polymerase to RNA sequence in transcription ?
sigma 70 or sigma factor in prokaryotic system | Like TBP in eukaryotic system
27
Explain the sigma cycle in prokaryotes
1) The binding of sigma factor to the promoter, brings in RNA polymerase 2) Two together they initiate the transcription process 3) As the transcription continues, polymerase leaves the promoter region and goes forward and sigma factor leaves( because his role is done) 4) To continue the transcription , NusA comes and helps the polymerase to continue transcription ( elongation) 5) When the transcription stops, NusA leaves and RNA polymerase is free to work again(termination)
28
Three types of RNA polymerase
Pol I: synthesis of rRNA Pol II: synthesis of mRNA and specialized RNA(microRNA,non-coding RNA) Pol III: synthesis of tRNA, 5s rRNA and specialized RNA
29
What is unique to transcription in eukaryotes
Initiator sequence which is at position +1( the first nucleotide transcribed) that has the transcription start site
30
What is meant by various regulatory sequences
In DNA promoter sequence to which TFs will come and bind and will regulate the transcription and multiple TFs can come
31
How many polymerases do eukaryotes and prokaryotes have
Eukaryotes- 3 | Prokaryotes -1 ( only Pol II)
32
How many subunits are there in RNA pol II in humans
12
33
What one extra step do transcription have comparing to prokaryotes
Assembly ( before initiation), because we need the preinitiation complex
34
RNA exit cleft where and what does it do
In RNA polymerase II and RNA is exiting through this cleft
35
What are two first proteins that come in the eukaryotic system when making a transcript?
TBP and TFIIB | and sometimes TBP comes with TFIID and TFIIA
36
The assembly in transcription is similar to
PIC in DNA replication
37
After all TFs come and bind , then
Polymerase II comes, bind to the promoter | more specifically preinitiation complex) and can start the transcription
38
How many nucleotides are usually open when transcribing and who does that
Approximately 17 nucleotides Polymerase II does it And now it is called transcription bubble
39
What is needed to be done to "move" polymerase II and start transcription
Modifications should take place in CTD( carboxyl-terminal domain) for the protein. It should be phosphorylated
40
What does TFIIH is doing in transcription
It phosphorylates CTD
41
After CTD is phosphorylated what happens
The polymerase escapes the promoter(start of the transcription) , as well as several TFs leave the system at all
42
WHen TFs leave, ___ come
Elongation factors come to help the transcription
43
How does termination occur
Elongation factor leave Termination factor come, they help pol II to stop transcribing, CTD is dephosphorylated, and the whole system is disassembled
44
What three modifications will be done to mRNA before it becomes mature and goes out in the cytoplasm
1. 5' cap 2. Polyadenylation 3. Slicing
45
When does 5' capping occur
Very early , only when 20-30 nucleotides are polymerized ( pol II is till working)
46
What is the purpose of 5' capping
To protect from ribonucleases
47
What is attached to mRNA during 5' capping
7 methylguanosine
48
What is the first nucleotide ( usually)
Adenine
49
What is the linkage in 5' cap
5',5' -triphosphate linkage
50
How does 5' capping occur by steps
1)gamma phosphate in Adenine ( which is in triphospahte form) is removed by phosphohydrolase 2) Guanylyltransferase attaches guanosine to the first nucleotide and removes two phosphate from guanosine ( as it comes in GTP form) 3) guanine-7-methyltransferase that adds methyl group to guanosine In some cases this enzyme can add methyl groups to the first few nucleotides
51
What part of PIC complex participate in 5' capping
CTD Synthesis of the cap is carried out by enzymes tethered to the CTD of Pol II.
52
Explain what happens at CTD
Cap synthesizing complex come in, performs ll the 5' capping stuff As soon as 5' cap is done , cap synthesizing system leaves as its function is done And then CBC( cap binding complex) comes and binds 5' cap to CTD, and this CBC will be there until the transcription is terminated)
53
What is the exception for introns
Histone gens do not have introns
54
Exons are ___, introns are __( length)
Exons-short | Introns-long
55
Explain self-splicing
Occurs in mitochondrial genes and do not require ATP the 3′-hydroxyl group of guanosine is used as a nucleophile in the first step of the splicing pathway. The guanosine 3′-hydroxyl group forms a normal 3′,5′-phosphodiester bond with the 5′ end of the intron . The 3′ hydroxyl of the exon that is displaced in this step then acts as a nucleophile in a similar reaction at the 3′ end of the intron. The result is precise excision of the intron and ligation of the exons.
56
What is typical to the gene that can undergo self splicing
It should have U- A at 5' end | and G-U and 3' end
57
What is the name of RNA prteoins that act as splicesome
snRNP's(snurp's)- small nuclear RNA that never leave nucleus
58
5 snurp's
U1, U2, U4,U5 and U6
59
Splicing by spliceosome occurs with __ introns and self splicing with ___
Self-splicing-> group 1 and 2(mRNA,tRNA and rRNA of bacteria, lower eikaryotes, higher plants) Splicing with spliceosome-> group 3 (mRNA) and 4(tRNA)
60
Spliceosomes has two parts :
Protein part and RNA part
61
Splicing by spliceosome require
ATP
62
3 important structures in spliceosome splicing
- 5' end of intron that has GU(donor site) - 3' end of intron that has AG(accepting site) - Upstream from 5' end there is a very important branching site with very important A in it
63
What happens when splicing with spliceosome
``` The U1 ( binds to donor site) and U2 (binds to A, branching site) snRNPs bind(ATP is used), then the remaining snRNPs (the U4-U6 complex and U5->U 5 goes to 3' end, acceptor site) bind to form an inactive spliceosome.( the addition always require ATP) The donor site and A site are brought together ( U1,U 4 dissociates and this requires ATP) ``` Lariat is formed ( a loop) between G of GU and A, a connection. This frees up 3' OH of the exon, which can now attack 5' end of the exon , connect with it And the rest Us leave with the lariat
64
Where does splicing with snurps occur
on CTD | The same CBC cap is attached as well.
65
Where do poly A tail is added
Transcribed beyond cleavage signal sequence , after 180 to 380 bases after the end sequence
66
What is the cleavage signal( nucleotide sequence)
AAUAAA
67
How does polyA tail is attached
Polyadenylate polymerase, endonuclease and many other proteins recognize the cleavage sequence and come to the transcription site. Endonuclease removes polymerase II and extra nucleotides Then polyadenylate polymerase adds multiple adenylate groups with usage of ATP

Biochemistry 2 (17 decks)

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