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MBG > Week 8 (Transcription and RNA Processing) > Flashcards

Week 8 (Transcription and RNA Processing) Flashcards

1
Q

RNA features

A

-has uracil in place of thymine
-has a ribose sugar (it bears a hydroxyl (–OH) group on its 2’ carbon)
* tertiary structure
* may interact as functional units (quaternary
structure)

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2
Q

Why is RNA unstable and why use it?

A

The presence of the unique 2’OH group in ribose causes it to react intramolecularly with the 3’OH site resulting in phosphate bond breakage

-can form many tertiary structures allowing it to have
different conformations for different functions
-easier to control, easily degraded

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3
Q

What is transcription

A

synthesis of RNA from DNA templates

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4
Q

How does RNA ultimately lead to protein?

A

RNA is transcribed into mRNA (messenger RNA), which is translated into a protein

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5
Q

components for transcription

A
  1. DNAtemplate
  2. 4 ribonucleosidetriphosphates
    (rNTPs)
    * A, U, C, G
    RNAn + rNTP RNAn+1 +PPi
  3. DNAdependant RNA polymerase
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6
Q

RNA Polymerase Holoenzyme subunit functions

A

alpha -involved in the assembly of the tetrameric core (2 of these)

beta – contains the ribonucleoside
triphosphate (rNTP) binding site

beta prime- contains the DNA template binding region

ω : (omega)-helps to stabilize the tetrameric core

sigma-binds to RNA polymerase
tetrameric core and assists in the correct
initiation of transcription specifically at the
promoter region of the prokaryotic gene. Many types of sigma factors → allows for specificity

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7
Q

Rho-INdependent Termination

A

Poly A sequence is transcribed into a poly U
tail after the hairpin is transcribed.
* pauses poly
* Hairpin forms and destabilizes the DNA-RNA hybrid
* Assisted by the weak A-U base pairing

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8
Q

Rho-dependent Termination

A

Two sequence features:
1) DNA sequence of terminator site causes Polymerase to pause
2) DNA sequence upstream of terminator encodes a stretch of RNA that is C rich and devoid of secondary structure.
a) Called the rho utilization (rut) site.
b) Rho binds to rut site
* Rho moves along RNA towards paused Polymerase
* Rho factor has helicase activity
* Unwinds the RNA-DNA hybrid
* Brings transcription to an end

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9
Q

What are the roles of specific promotor sequences in eukaryotic transcription?

A

-special promoter sequences for genes transcribed by RNA poly I, II, or III
-accessory proteins recognize the specific promoters and recruit the appropriate poly to beign transcription

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10
Q

Transcription in Eukaryotes-Initiation

A

-assembly of transcription factors of Pol II (TFIID)
-TFIID complex contains TATA binding protein, assembles at TATA box followed by remaining TF’s and Pol II, causes DNA to unwind
-forms preinitaiton complex

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11
Q

Transcription in Eukaryotes-elongation

A

-poly moves along template strand leaving TF intact at promoter
-maintains rNTO transcription bubble
-hybrid bends at right angle
-positions -OH group at active site where nucelotides are added
-newly synthesized RNA separated from DNA and exits throguh cleft

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12
Q

Transcription in Eukaryotes-termination

A

-RNA Pol I:
requires a termination factor similar to rho factor in prokaryotes.
-RNA Pol II: transcription
continues past termination
sequence.
- RNA is cleaved at a
consensus sequence in the R
RNA Pol III: ends after transcribing a terminator sequence that produces a string of U’s that is downstream from a hairpin. Similar to rho-independent termination.

Cleaved RNA=2 RNAs: one
that will encode a protein and the
other with its 5’ trailing out of the
RNA polymerase.
* Rat1 (5’→ 3’ exonuclease) attaches
to 5’ end, degrades remaining RNA strand
* Transcription is stopped when
Rat1 reaches transcription
machinery

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13
Q

Transcription in Prokaryotes-Initiation

A

-sigma factor associates with core enzyme to form a holoenzyme which binds to -35 and -10 consensus sequences in promotor
-RNA poly positions over start site, and unwinds DNA to produce single-stranded template
-Initiation: RNA polymerase binds, unwinds and joins first 2 nucleotides (no primer)

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14
Q

Transcription in Prokaryotes-Elongation

A

-Elongation: when Sigma factor is released and RNA poly moves along the 3’ to 5’ DNA template strand. Nucleotides continuously added. RNA poly generates transcription bubble that moves with RNA poly

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15
Q

Transcription in Prokaryotes-Termination

A

-Termination: when RNA polymerase reaches “terminator” region of the gene.
* Occurs upstream of where the actual termination will take place.
* The newly-synthesized RNA together with the RNA polymerase are released.
* Bacterial cells possess two major types of terminators:
Rho-dependent (requires Rho factor) and Rho-
independent (aka intrinsic terminator)

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16
Q

exons

A

-protein coding segments
-vary in length and position on gene

17
Q

What does RNA processing require in eukaryotes

A

pre-mRNA is produced from a template strand of a gene being transcribed, then is processed to make mature messenger RNA (mRNA) that can be translated into a protein

18
Q

Three primary regions of a mature mRNA

A
  • 5’ untranslated region (5’UTR): does not code for amino acids. Binds the
    ribosomal complex.
  • Protein coding region: comprises the codons that specify the amino acids.
    Begins with a start codon and ends with a stop codon.
  • 3’ UTR: does not code for amino acids. Affects the stability of the mRNA and
    regulates its translation.
19
Q

introns

A

-intervening (non-coding) segments
-can influence how genes make proteins or how non-coding RNA are expressed
-present on eukaryotic DNA, can vary in nucleotide length
-removed from pre-mRNA by action of a spliceosome
-has 3 conserved sequences:
1. 5’ splice sequences containing the junction sequences GU
2. 3’ splice sequence containing the junction seequence AG
3. intron branch point: a conserved “A” residue located upstream of 3’ splice site

20
Q

addition of 5’ cap

A

facilitates binding of ribosome to 5’ end of mRNA, increases mRNA
-Addition of 7-Methyl Guanosine (7-
MG) Cap
-Linked to pre-mRNA by linkage between the 5’ P of the 7-MG and the 5’ P of the first ribonucleotide in the RNA (5’ to 5’phosphate
linkage)

20
Q

3’ cleavage and addition of poly A tail

A

increases stability of mRNA, facilitates binding of ribosome to mRNA

-A’s added w/o template
-“polydenylation”

21
Q

RNA splicing

A

removes noncoding introns from pre-mRNA, facilitates export of mRNA to cytoplasm, allows for multiple proteins to be produced

-removal of introns from pre-mRNA, must be precise to properly fuse the 3’ end of one exon to the 5’ end of the next exon
1. U1+U2 bind
2. U4, U5, U6 join complex. changes shape + proximity of U2+U6
3. U1 + U4 released
4. remaining spliceosome held by RNA base pairing
5. following cleavage, intron binds (lariat) and exons join (w p-bonds)
6. introns released

22
Q

spliceosome

A

-RNA/protein structure
-has 5 snRNAs (small nuclear RNAs) that associate with 300 small proteins to form snRNP (small nuclear ribonucleoproteins

23
Q

spliceosome assembly

A

-snRNA of spliceosome form complimentary base pairing with pre-mRNA
-cataylytic steps carried out y snRNAs of the spliceosome
-addition of U4, U5 and U6 join the spliceosome
-U4, U5, U6 cause shape change
-U1 and U4 dissociate
-base pairing occurs between mRNA and snRNA sequences that hold the splcieosome together
-2 transesterification rxn by U6, joins 2 exons together and releases the lariat

24
Q

alternative processing pathways

A

alternative splicing (introns)

-pre-mRNA processed to produce diff types of mRNA
-produces diff proteins from same DNA sequence

multiple 3’ cleavage site (exons):

-can generate longer/shorter exon (on last exon)
-may or may not produce diff protein

25
Q

RNA editing

A

changes gene content via

-editing mRNA by endogenous guide RNAs
-inserting/deleting uridine monophosphate residues
-changes structure of individual bases (tRNAs, mRNAs)

26
Q

what are endogenous guide RNAs and nucleotide addition in RNA processing

A

-gRNAs made in cell direct insertion of uridine bases into mRNA by repair polymerase
-permanently modifies the mRNA by making new codons that specify new amino acids

27
Q

tRNA modifications

A

-anticodon of tRNA base pairs with mRNA codon
-amino acid covalently attached to tRNA 3’ end
-contain modified ribonucleotides through modifying enzymes
(extra 3’ and 5’ sequences removed, introns removed)

28
Q

snRNA

A

small nuclear RNA

-acts in complex with proteins
-plays role in post-transcriptional processing of RNA (splcing)

29
Q

snoRNA

A

small nucleolar RNA

-act in complex with proteins
-in eukaryotes, guide enzymatic chemical mods of ribosomal RNA in nucleolus

30
Q

SiRNA and miRNA

A

small interfering RNA and micro RNAs

-in eukaryote as double-stranded RNA
-act as short, single stranded RNAs, binds to complementary sequences in mRNA
-produced by mRNA cleavage, RNA transposons + RNA viruses
-regulates gene expression

31
Q

crisprRNA

A

in prokaryotes
-encoded by DNA sequences in rokaryotes genomes
-works with Cas9 nuclease to cleavage foreign DNA

32
Q

long-non coding RNA

A

in eukaryotic cells
-regulate gene expression at transcription and translation level by binding mRNA or isolating micro-RNAs that control gene expression

MBG (3 decks)

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