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Micro 265 Fall 2023 > 4.1 - Transcription > Flashcards

4.1 - Transcription Flashcards

1
Q

What is a promotor?

A

it tell you where to start and it also tell you which direction you need to go into. (indicated by a +1)

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2
Q

What is a transcriptional terminator?

A

a stop codon, it tells you to stop the transcription.

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3
Q

What is transcription in a brief manner?

A

it is the first step.

DNA –> RNA

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4
Q

What is translation in a brief manner?

A

it is the second step.

RNA –> protein

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5
Q

What enzyme does transcription use?

A
  • it used RNA polymerase.
  • this enzyme builds RNA from DNA template.
  • it binds to DNA template and makes one copy of DNA from 2 strands.
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6
Q

What does RNA polymerase do?

A
  • it binds to DNA template and makes an RNA copy of one of two strands.

-copied strand = coping strand

  • the other strand = template strand.
  • it only builds RNAs 5’ to 3’, as it only goes in one direction.
  • Because DNA strands run opposite (5’ to 3’), transcription from two DNA strands goes in opposite directions.
  • the top strand is 5’ to 3’ and the bottom strand is 3’ to 5’
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7
Q

Steps of transcription:

A

step 1:Initiation is the beginning of transcription. It occurs when the enzyme RNA polymerase binds to a region of a gene called the promoter. This signals the DNA to unwind so the enzyme can ‘‘read’’ the bases in one of the DNA strands. The enzyme is now ready to make a strand of mRNA with a complementary sequence of bases.

Step 2: Elongation
Elongation is the addition of nucleotides to the mRNA strand. RNA polymerase reads the unwound DNA strand and builds the mRNA molecule, using complementary base pairs. During this process, an adenine (A) in the DNA binds to an uracil (U) in the RNA.

Step 3: Termination
Termination is the ending of transcription, and occurs when RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA.

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8
Q

what enzyme is used in transcription in bacteria?

A
  • RNA polymerase core enzyme is use .
  • This enzyme goes through and builds RNA chain.
  • The RNA polymerase is build up of 5 subunits: alpha, beta, beta prime, and omega (w).
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9
Q

what is an additional subunit?

A
  • Holoenzyme (sigma).
  • only RNA polymerase first initiated the transcription process.
  • This sigma factor interacts for only a brief period of time.
  • the RNA polymerase tries to find a promotor.
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10
Q

what does the sigma factor do?

A
  • it binds the to promoter region and then dissociates from core enzyme.
  • it brings the promoter region to RNA polymerase.
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11
Q

what does the core enzyme do?

A
  • it unwinds DNA to expose a template which then forms a transcription bubble.
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12
Q

How is the RNA chain built?

A
  • Using NTPs (ATP, CTP, GTP, UTP) as. substrates and the template strand as a guide to building the RNA chain one nucleotide at a time.
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13
Q

How are the NTPs used?

A
  • so basically 2 phosphate are burned off which provides energy.
  • the single leftover phosphate is then added to the 3’OH.
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14
Q

how is the RNA released?

A
  • the RNA polymerase will encounter a transcriptional terminator and will dissociate from the template and release the RNA.
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15
Q

Steps to how RNA is released?

A
  1. sigma recognizes promoter and initiation site.
  2. transcription begins, the sigma is released and then the RNA chain grows.
  3. The termination site is reached and the chain growth stops.
  4. polymerase and RNA is released.
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16
Q

what is a transcriptional terminator?

A
  • it helps RNA polymerase dissociate from DNA and then eventually stops making RNA and releases transcript.
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17
Q

what are the two ways that a trancriptional terminator happens?

A
  1. Intrinsic (rho-independent) terminator
  2. Rho-dependent terminator
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18
Q

what happens in the intrinsic terminator?

A
  • it occurs when RNA hairpin structure forms, followed by a string of U residues.
  • the U residues act as a pause signal for RNA polymerase (formation of hairpin forces RNAP off template)
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19
Q

what happens in Rho-dependent terminators?

A
  • the Rho protein binds to RNA as it is being transcribed and causes the RNA polymerase to dissociate after it encounters certain sequences.
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20
Q

what are the steps that lead to intrinsic terminator?

A
  • transcription of the lower strand the one from 3’ to 5’.
  • the Rna forms a secondary structure. When it hits the strings of U’s it forms a hairpin.
  • the stem-loop in RNA immediately upstream from a run of uracils leads to intrinsic transcription terminator.
21
Q

what is a promoter?

A

Transcriptional initiation is guided by DNA sequences

22
Q

what is dictated by the binding of sigma factors?

A
  1. Whether or not a sequence acts as a promotor/if promoter is active is
  2. the activity of regulatory proteins
23
Q

Do bacteria encode multiple different sigma factors?

A

yes, Bacteria encode multiple different sigma factors that are produced under
different conditions. They recognize different sequences (promoters)

24
Q

what is the housekeeping sigma factor called?

A
  • sigma 70 or RpoD
  • it recognizes two sequences upstream of the
    transcriptional start site.
25
Q

Are sequences degenerate?

A
  • yes, – don’t usually match exactly. It can be
    difficult to find an RpoD promoter by looking at raw sequence
26
Q

What does the RpoD promoter have?

A
  • it has 2 sequences ( one is -35 (+1 site) and one is pribnow.
  • the RNA polymerase interacts with both sequences
  • the sequences do not follow a consensus sequence.
27
Q

Other factors

A
  • RpoD is very general
  • there are other sigma factors that work in the same way for RNA polymerase but have a specialized function.
  • ex. sigma 38 is good for keeping a cell stationary, and it is basically when they recognize that it is not a good time to grow.
28
Q

what is upstream?

A
  • sequences or letter code before the gene
  • it goes towards the left direction
29
Q

what is downstream?

A
  • sequences or letter codes after the gene
  • it goes towards the right.
30
Q

example of upstream and downstream.

A
  • The promotor is the start site of where DNA goes to RNA, and is used to figure out where everything else goes.
  • if there is a -1 then it is upstream as it is before the gene.
  • if there is a +2 then it is downstream as it is after the gene.
31
Q

what are the three classes of RNAs?

A
  1. Messenger RNA (mRNA):
  2. Transfer RNA (tRNA)
  3. Ribosomal RNA (rRNA)
32
Q

Note to classes of RNA

A
  • there are other non-coding RNA with a range of functions that are often regulatory but do not fall in any of the three catgeories.
33
Q

what is mRNA?

A

-converts to protein via translation.

34
Q

what is tRNA?

A

functional RNAs, used in translation

35
Q

what is rRNA?

A

functional RNAs used in translation

36
Q

what is the 95% of cells in RNA made up of?

A
  • made up of rRNA and tRNA.
  • both rRNA and tRNA are highly transcribed genes.
37
Q

what do mRNA contain?

A

1.Open reading frames (ORFs)
a. part that gets translated to protein.
2. untranslated regions (UTRs)
a. part that is not translated.

38
Q

what are polycristrinic?

A

-mRNAs that encode multiple ORFs

  • polycistronic means more than on cistron
39
Q

what is contranscribed?

A
  • such genes are arranged in an operon.
  • the genes in an operon are cotrasncribed.
  • means it is transcribed together.
39
Q

what is an operon?

A
  • a bunch of genes driven by a single promoter.
39
Q

what is involved in a simple mRNA encoding a single reading frame?(ORF)

A
  1. 5’UTR –> everything from first transcribed residue (+1) through the start
    codon of gene. Contains ribosome binding site (RBS),
  2. ORF –> Start codon (e.g. ATG) through stop codon (e.g. TAA)
  3. 3’ UTR –> everything from the stop codon of the gene through the final
    transcribed residue. Often contains transcriptional terminator sequences
39
Q

what are some ways transcription is different in eukaryotes?

A
  1. have 3 RNA polymerases. RNA polymerase II produces mRNA(encode proteins). Others encode RNA transcripts that are not translated
    a. multiple polymerase do this job
  2. Eukaryotic RNA polymerases are more complex – 12+ subunits (bigger and more complex)
  3. RNAP require transcription factors to recognize
    promoters, which they bind specific DNA sequences & recruit RNA polymerase (usually sigma factor but many more)
    a. TATA box bound by TATA-binding transcription factors.
  4. Eukaryotes do not use operons – each gene has its own promoter
  5. primary mRNA transcripts contain protein-coding exons and noncoding introns. mRNAs are processed (spliced) to remove introns
    a. lots of processing
  6. Eukaryotic mRNAs are polyadenylated at the end (3’) of transcript and capped
    at 5’ end using a modified G residues attached using an unusual linkage
  7. Eukaryotic mRNAs transcribed/spliced in nucleus, translated in cytoplasm
    a. they are separated out from translation.
    b. IN BACTERIA TRANSCRIPTION OCCURS AT THE SAME TIME AS TRANSLATION
40
Q

Steps of transcript processing in eukaryotes?

A
  1. addition of 5’ cap an 3’poladenylation in nucleus
  2. introns excised or removed in nucleus
  3. mRNA is exported to the cytoplasm and translated to protein.
40
Q

What does the archeal RNA polymerase resemble?

A
  • resembles RNA polymerase II from eukaryotes and has 11-13 subunits.
  • Is also recruited to promoters using
    transcription factors – many of which are related to eukaryotic proteins.
41
Q

what does archaea also use?

A
  • TATA boxes & transcription factors that bind these
    elements & recruit RNA polymerase.
42
Q

is transcription in archaea similar to bacteria?

A
  • Others aspects of transcription in archaea more like bacteria…mostly in
    terms of “simplicity”
43
Q

what are the key points of archaea transcription (like bacteria)?

A

-No 5’ cap, no poly A tail, mRNAs do not have introns & are not
spliced

  • No nucleus – transcription and translation often coupled (like in
    bacteria
44
Q

what do archaea also use that eukaryotes don’t use ?

A
  • operons, just like how bacteria use it.
  • operon (multiple genes encoded by one
    RNA (single promoter controls expression of several genes))
45
Q

Is archaea a less complex version of eukaryotic transcription?

A

yes, archaea is less complex than eukaryotes in terms of transcriptions.

Micro 265 Fall 2023 (9 decks)

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