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MBIO2020 > 1.3 - Transcription > Flashcards

1.3 - Transcription Flashcards

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1
Q

how does the change of deoxyribose to ribose affect the chemistry of the nucleic acid?

A

-enzymes that act on DNA usually have no effect on RNA and vice versa

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2
Q

what are the primary and secondary structures of RNA?

A

-predominantly exists in single strands (primary)
-folds back upon itself where complementary base pairing is possible aka inverted repeats form a hairpin structure (secondary structure)

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3
Q

what type of molecule is RNA? how does this differ from DNA?

A

-RNA is both a genetic AND functional molecule
-DNA is strictly a genetic molecule

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4
Q

what are the 3 major types of RNA and their abundances within the cytosol at any given moment?

A

-messenger RNA (1-2%)
-transfer RNA (15%)
-ribosomal RNA (85%)

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5
Q

how does the structure of RNA affect its longevity?

A

-mRNA typically are only in a primary structure so they only last a few minutes before being degraded by ribonucleases
-tRNA and rRNA are both long-lived because they have secondary structures which prevent ribonucleases from attacking

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6
Q

what is the role of mRNA?

A

-carries genetic information from the genome to the ribosome (completes the central dogma)

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7
Q

what is the role of rRNA?

A

-structural and functional in ribosomes for protein synthesis

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8
Q

what is the role of tRNA?

A

-active role in carrying amino acids for protein synthesis

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9
Q

how does RNA polymerase work to catalyze transcription?

A

-does not need a primer to start
-energy to to polymerize is given through the hydrolysis of 2 energy rich phosphate bonds of the incoming ribonucleoside triphosphates (ATP, GTP, UTP, CTP)
-once the triphosphates bond (added to the 3’ OH of ribose), 2 of the phosphate bonds are cleaved off (hence a release of energy)

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10
Q

what is a basic overview of the transcription process?

A

-RNA polymerase and sigma factor binds to the promoter region of the DNA
-transcription begins and sigma factor dissociates (reading 3’-5’ and working 5’-3’)
-no primer or helicase is needed (RNA polymerase moves along the DNA strand as it elongates the mRNA and DNA reforms its helix right after it leaves, no breaking needed)
-when the termination site is reached, dissociation of RNA polymerase and mRNA occurs

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11
Q

what are the 2 strands in transcription?

A

-template strand (non-coding)
-non-template strand (coding)
-the coding strand will have the same nucleotide seqeunce as the mRNA that gets transcribed (except U’s instead of T’s)
-the mRNA is complementary to the template strand
-strands are named based on the gene, not the DNA strand itself

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12
Q

what strand contains the gene?

A

-the coding strand
-genes are read as 5’-3’
-the template strand is read as 3’-5’ (5’-3’ strand is worked by RNA polymerase)

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13
Q

what is the role of RNA polymerase? what is its structure?

A

-performs transcription (elongation)
-large multimeric enzyme (core enzyme) that has catalytic activity
-2 alpha, 1 beta, 1 beta prime, and 1 omega subunit
-has quaternary structure (multiple polypeptides coming together)

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14
Q

what is significant to note about the beta subunit in RNA polymerase?

A

-the beta subunit is the target site of the rifamycin class of antibiotics which would lead to an inhibition of RNA synthesis

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15
Q

what 2 parts make up the transcription apparatus?

A

-RNA polymerase
-sigma factor
-together form a holoenzyme (fully functional)

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16
Q

what is the role of sigma factor in the transcription apparatus?

A

-controls the binding of RNA polymerase to the promoter
-detaches once the first few RNA nucleotides have joined together
-multiple types of sigma factors and can bacteria can carry multiple

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17
Q

what does the different types of sigma factors control?

A

-controls the set of promotors that the RNA polymerase can bind to
-example = sigma factor 70 (RpoD)

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18
Q

what are the 3 stages of transcription?

A

-initiation
-elongation
-termination

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19
Q

what does it mean for something to be upstream of a gene?

Study These Flashcards
A

-located before (closer to the 5’ end)

20
Q

what are the 2 boxes located in the promotor region? what is their role in transcription?

Study These Flashcards
A
  • -35 box (upstream from -10 box)
  • -10 (pribnow box)
    -act as landing sites of recognition (lands on the -35 first and then the -10)
  • -10 is where the DNA begins to unwind (upstream of the +1 site aka first nucleotide of the RNA chain)
21
Q

what are consenus box sequences?

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A

-sequences that are typically the same or conserved
-derived from comparison of promotor regions
-ex: -35 = TTGACA -10 = TATAAT in E.coli chromosome (sigma 70)

22
Q

what is the function of the genes of the sigma factor 70 and TTGACA sequence?

Study These Flashcards
A

-for most genes (major housekeeping genes for normal growth)

23
Q

what is the promotor region of a gene?

Study These Flashcards
A

-contains elements essential for transcription (-35 and -10 boxes)
-the recognition and binding site for RNA polymerase holoenzyme
-AT rich regions because they are easier to break (specifically -10 pribnow box)

24
Q

what is the leader sequence of a gene?

Study These Flashcards
A

-downstream from the promotor region
-gets transcribed into mRNA but not translated
-transcription beings here (+1 position, with usually purines)

25
what is the coding region of a gene?
-downstream from the leader sequence -transcribed and translated into a polypeptide (protein)
26
what is the trailer region of a gene?
-downstream from the coding region -transcribed into mRNA but not translated -portion that prepares RNA polymerase to release the template strand
27
what is the terminator region of a gene?
-downstream from the trailer region -where the RNA polymerase relases the template strand
28
which of the 2 boxes in the promotor region is sigma factor specific?
- -35 box
29
what do variations in the sequences in the promotor regions cause?
-a change in promotor strength (ease of RNA polymermase holoenzyme recognizing/binding)
30
what is a closed complex in transcription initiation?
-formed from the first recognition and binding of RNA polymerase holoenzyme to the promotor region -closed complex because the DNA is still double stranded
31
what is an open complex in transcription initiation?
-formed due to the "melting" of the -10 pribnow box region -forms the transcription bubble (16-20 bp) -polymerization of the first few RNA nucleotides occurs
32
what is the process of transcription elongation?
-the core RNA polymerase enzyme will read the template strand of DNA in the 3'-5' direction -RNA will be synthesized in the 5'-3' direction (new nucleotides going at the 3' end) -ribonucleotide triphosphates are added (bonds get cleaved, so chain is made of ribonucleotide monophosphates) -there is a temportary phase of a double stranded RNA/DNA hybrid (RNA transcript eventually seperates from the template and the ssDNA rewinds to from the double helix structure)
33
what is special about the process of transcription?
-it is a repetitive process when conditions permit -therefore initiation does not depend on the completion of a previous round of transcription (can do multiple at once) -on a micrograph, shorter transcripts will hint that they have only just started and longer transcripts will hint that they have been going for a while
34
what first signals transcription termination?
-inverted repeats at the end of a gene sequence on the coding strand (central non-repeating unit between) (G + C rich signal) -when transcribed a hairpin/stemloop structure is formed
35
how does the hairpin structure initiate termination?
-presents as a physical obstruction which causes RNA polymerase to stall temporarily
36
what are the 2 mechanisms that can allow RNA polymerase to be removed from the template strand? what can happen in either case?
-rho independent termination -rho dependant termination -core RNA polymerase can re-associate with sigma factor to form the holoenzyme and initiate transcription again
37
what is the rho independent mechanism of termination?
-there is an A-rich region present after the inverted repeats in DNA (weaker bonds making it easier to dissociate) -string of U's form in the RNA following the hairpin structure -causes destabilization of the RNA/DNA hybrid in the open complex (U is not typical in DNA so it is not able to hold the hybrid together) -this results in RNA polymerase releasing -intrinsic terminator because no special protein is needed as it is built into the DNA sequence
38
what is the rho dependent mechanism of termination?
-a special protein is required (rho) -there is a rut site within the mRNA transcript (not active in DNA, but it is encoded) -once transcribed this site will be bound by multi-rho hexameric protein that assembles around the RNA transcript (helicase-like activity that is fuelled by ATP hydrolysis) -this protein moves in the 5'-3' direction along the transcript -when the hairpin structure (terminator) occurs the RNA polymerase slows and pauses, allowing the rho protein to catch up and knock the polymerase off the strand (also destabilizes the hybrid region)
39
what types of transcriptional units are there?
-monocistronic transcript -polycistronic transcript -non-translated RNAs
40
what is a monocistronic transcriptional unit?
-RNA transcribed from a single gene -has its own promotor and terminator -most common
41
what is a polycistronic transcriptional unit?
-formed from two or more genes (co-transcribed) -ex: operons -contain multiple ribosome binding sites that are upstream of the coding sequences to facilitate translation (protein synthesis, makes separate proteins) -transcribed and translated sequentially by the same ribosome
42
what are non-translated RNAs?
-tRNAs -rRNAs -non-coding RNAs (regulatory roles)
43
what is an operon's structure?
-two or more genes with one promotor and one terminator
44
how does an operon of polycistronic RNA that is translated work?
-contain multiple ribosome binding sites that are upstream of the coding sequences to facilitate translation (protein synthesis, makes separate proteins) -transcribed and translated sequentially by the same ribosome -contains spacers between the genes
45
how does an operon of polycistronic RNA that is not translated work?
-all genes are transcribed from a single promotor in a coordinated synthesis -the primary transcript is cleaved by ribonucleases -spacers are discarded
46
what do we call RNA that has a post modification?
- pre-RNA

MBIO2020 (12 decks)

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