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MBG 2040 Molecular Biology > Chapters 13 & 14: Transcription and RNA processing > Flashcards

Chapters 13 & 14: Transcription and RNA processing Flashcards

1
Q

What are the 5 basic rna features?

A
  1. rna has ribose sugar, has OH on 2’ carbon
  2. contains uracil in place of thymine
  3. tertiary structure
  4. can interact as functional units
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2
Q

Why is rna less stable than dna?

A

presence of 2’OH causes it to react intramolecularly with 3’OH site resulting in instability

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3
Q

what is the only rna that is coded for proteins?

A

mRNA

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4
Q

In which direction is rna synthesized?

A

5’->3’

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5
Q

Which dna strand does rna use for synthesis?

A

3’->5’ dna strand

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6
Q

What is the template and non template strand in txn?

A

template - 3’->5’
non template - 5’->3’

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7
Q

What is the chemical reaction for rna synthesis?

A

RNAn + rNTP -> RNAn+1 + PPi

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8
Q

What are the four general features of rna synthesis?

A
  1. rNTP is the precursor
  2. only one strand of dna is used
  3. rna synthesis does not need a primer to initiate
  4. rna synthesis is catalyzed by pol
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9
Q

What is the core rna pol vs the rna pol holoenzyme?

A

core rna pol - has beta, beta prime, two alphas, omega
holoenzyme - everything just add sigma factor

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10
Q

What are all the functions of the holoenzyme subunits?

A

alpha - assembles tetrameric core
beta - contains rNTP binding site
beta prime - contains dna template binding region
omega - stabilize tetrameric core
sigma - binds to rna pol tetrameric core and assists in correct initiation of txn

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11
Q

what does the sigma factor do?

A

binds to -35 and -10 consensus sequences in promoter region

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12
Q

which strand are the consensus sequences on?

A

5’->3’ NT

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13
Q

What are the steps to initiation in txn in prok?

A

once holoenzyme is bound to promoter, rna pol is position over the txn start site (+1) and unwinds dna to produce single strand

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14
Q

what are the steps (5) to elongation in txn in prok?

A
  1. holoenzyme binds to promoter tightly and unwinds dna
  2. rNTP complementary to base at start site serves as first nucleotide (Base-P-P-P)
  3. two phosphate groups leave rNTP (PPi)
  4. sigma factor leaves
  5. new nucleotides are added
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15
Q

What are the steps (2) to termination in txn in prok?

A
  1. txn stops when rna pol reaches terminator region
  2. new rna strand and pol are released in 1 of 2 methods
    • Rho dependent term
    • Rho independent term
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16
Q

What is rho dependent termination?

A

rho binds to rut site (C-rich) on rna strand and moves up rna. It uses helicase activity to unwind rna-dna strands and releases rna

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17
Q

What is rho independent termination?

A

inverted repeats are transcribed into rna and a poly a tail on dna. inverted repeats fold into a hairpin which destabilizes the UUUUU-AAAAA pairing, which releases the rna molecule

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18
Q

How do pol in txn in euk bind and begin txn?

A

promoter dna sequences are recognized by accessory proteins (TF) which bind to regions and recruit pols (specific) to them

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19
Q

What does a promoter consist of in euk txn?

A

regulatory promoter and core promoter (-35, -25 (TATA), +1 start, +30)

20
Q

What are the steps (4) to initiation in txn in euk?

A
  1. TDIID binds to TATA box in the core promoter (TFIID has tata binding protein (TBP))
  2. TF’s and RNA pol bind to the core promoter - this is called the pre-initiation complex
  3. TF’s bind to enhancer sequences
  4. DNA loops out, allowing proteins bound to enhancer to interact with basal txn apparatus
21
Q

What are the steps (2) to elongation in txn in euk?

A
  1. polymerase moves along template strand leaving txn factors intact at promoter for reinitiation of txn w new pol
  2. newly synthesized rna is separated from dna and exits through another cleft
22
Q

What are the steps to termination in txn in euk?

A
  1. Depending on the Pol that is transcribing
    • pol I: requires termination factor like rho
    • pol III: similar to rho indep
    • pol II: txn continues past termination sequence but rna is cleaved and a tail is hanging out of pol, which required a rat 1 (5’->3’ exo) that attaches to the 5’ end of the rna tail and chews up rna, txn is terminated once rat 1 reaches end
23
Q

What is the shine-delgarno sequence?

A

prok
short sequence before the start codon

24
Q

What the the three primary regions on mature mRNA?

A

5’ UTR - binds ribosomal complex
Protein coding region - begins with start ends with stop, codes for aa
3’ UTR - affects stability and regulates tln

25
Q

what are exons vs introns?

A

exons are protein coding segments, introns are non coding segments

26
Q

where does splicing take place?

A

in the nucleus

27
Q

what are the three main processing steps in euk pre mRNA?

A
  1. addition of 7-methyl guanosine cap to 5’ end
  2. addition of poly-A tail to 3’ end
  3. removal of introns by splicing
28
Q

How is the 5’ cap made?

A

4 methylations occur on the structure (know)

29
Q

How is the 3’ poly-A tail made?

A

once poly-A consensus sequence is recognized, poly-A pol will make poly-A tail 11-30 nt downstream

30
Q

What are the three conserved sequences that are required for splicing?

A
  1. 5’ (end of intron) splice sequences at very end is GU
  2. 3’ splice sequence containing junction sequences AG
  3. intron branch point A
31
Q

What are the steps (3) to rna splicing?

A
  1. pre-mRNA is cute at 5’ splice site and the 5’ end of intron attaches to branch point (lariat-> 5’ phosphate of G nt binds to 2’ OH of A nt)
  2. cut is made at 3’ splice site and simultaneously the 3’ end of exo 1 becomes covalently attached to 5’ end of exon 2
  3. intron (lariat) is degraded
32
Q

What is a spliceosome?

A

Protein structure that contains 5 small snRNAs (U1,U2,U4,U5,U6) - cuts the pre mrna

33
Q

How do the snRNAS of the spliceosome cut the pre mRNA during splicing?

A

U1 - attaches to 5’ splice site
U2 - attaches to branch point
U4,U5,U6 complex cause conformational change and bring 5’ splice site to branch point
U1 and U4 dissociate
base pairing occurs between U6 and U2 and between U6 and 5’ splice site
exon 2 is released

34
Q

What is alternative splicing?

A

Pre-mRNA can be processed in different ways to produce alternative types of mRNA, exons are included or excluded - which results in different proteins

35
Q

What is multiple 3’ cleavage sites?

A

generates a longer or shorter exon, occurs in the last exon

36
Q

What are gRNA’s and how do they edit rna?

A

guide rnas direct the insertion of uridine bases into the mRNA by pol. creates new codons

37
Q

What is ApoB and how does it contribute to rna editing?

A

Blood proteins that carry fat in blood stream; cytidine deaminase changes C to U which changes the protein

38
Q

What are tRNA modifications and how do they contribute to rna editing?

A

modifications of bases in tRNA creates mature tRNA with amino acid on the end

39
Q

What are ribosomes and how are they made?

A

Have large and small subunits and are assembled by rRNA

40
Q

What are the rRNA synthesis sites in euk and prok?

A

euk - nucleolus
prok - cytoplasm

41
Q

What are snRNA’s?

A

small nuclear rnas - spliceosomes
play roles in splicing

42
Q

what are snoRNA’s?

A

guide modifications of rRNA’s tRNA’s and snRNA’s

43
Q

what are siRNA and miRNA?

A

found in euk, regulate gene expression, bind to complementary sequences in mRNA

44
Q

what is Crispr RNA?

A

found in prok

45
Q

What are LncRNA?

A

euk, control gene expression

MBG 2040 Molecular Biology (4 decks)

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