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Genetik > Dna Transcription > Flashcards

Dna Transcription Flashcards

1
Q

information flow in the central dogma

A
  1. DNA replication (DNA -> DNA)
  2. Transcription (DNA -> RNA)
  3. Translation (RNA -> Protein)
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2
Q

in all living organisms, genetic information flows…

A

…from DNA to RNA to Proteins in a unidirectional pathway

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3
Q

exceptions to the central dogma

A

information between nucleic acids is flexible
1. RNA replication: RNA can make RNA (eg: RNA viruses)
2. reverse transcription: RNA can make DNA (eg: telomerase)

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4
Q

is translation unidirectional

A

yes, translation has so far proven to be unidirectional

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5
Q

RNA is the essential…

A

…intermediate between DNA and proteins

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6
Q

RNA primary structure

A
  1. four different nucleotides
  2. each nucleotide contains one base, ribose, phosphate
  3. joined through phosphodiester bonds
  4. polarity from 5’ -> to 3’
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7
Q

what are the consequences of the differences in primary structure between RNA and DNA

A
  1. T (5-methyl-U) and U both base pair with A
  2. the presence of 2’ OH makes RNA sugar-phosphate backbone more sensitive to hydrolysis
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8
Q

RNA secondary structure

A
  1. very different to DNA
  2. contains only one strand which makes them very flexible
  3. RNA molecules can make intramolecular base pairs on the same strands -> creating crazy structures like hairpins, stems etc due to palindromes
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9
Q

base pairing rules in RNA

A
  1. same as in DNA meaning Chargaffs rules apply here as well
  2. A-U, G-C
  3. The only exception is that G can technically base pair with U; they don’t contribute to stability
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10
Q

stability of stems

A

depends on
1. length: long > short
2. sequence (number of hydrogen bonds): GC>AU>GU

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11
Q

Palindromes

A

a word or a phrase that reads the same forwards and backwards

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12
Q

palindromes in DNA sequence

A

sequences where the same sequence is found not on the same strand, but rather on the complementary strands

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13
Q

complex 3d structures of RNA

A
  1. can be stably folded into complex structures
  2. this freedom allows RNA to develop catalytic abilities -> ribozymes
  3. RNA catalyses some of the key reactions in RNA processing and translation
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14
Q

transcription definition

A

synthesis of RNA from a DNA template

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15
Q

RNA transcription requirements

A
  1. ssDNA
  2. activated (triphosphate) nucleotide precursors
  3. transcription proteins (RNA polymerase)
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16
Q

RNA polymerases

A

transcription protein in RNA transcription that can start new chains

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17
Q

Biochemistry of polymerization

A
  1. free 3’ OH attacks alpha phosphate
  2. release of pyrophosphate (PPi)
  3. Hydrolysis of PPi
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18
Q
A
19
Q

What is RNA catalyst

A

Is a ribozyme that catalyzes many key reactions during processing and translation

20
Q

Transcription in rna vs dna

A

Transcription is basically the same. However, rna polymerase unwinds dna helix itself, and always the same strand is transcribed for a gene

21
Q

What is required for transcription

A
  1. Different accessory proteins
  2. Transcription bubble
  3. Does not require a primer
22
Q

Transcription in E.coli initiation

A
  1. Sigma factor associates with core RNA polymerase
  2. Holoenzyme binds to promoter
  3. Sigma factor promotes melting of dna, which generates an open complex
  4. First nucleotide binds to +1 position, and second one binds as well
  5. Rna pol catalzys first phosphordiester bond
  6. Core polymerase escapes from promoter, and only Sigma factor is left behind
23
Q

Promoter recognition in E.coli

A

The promoter has a consensus sequence that the holoenzyme binds to. Different sigma factors will recognise different consensus sequences

24
Q

What determines how well the holoenzyme binds to the promoter

A

Spacing between -35 and -10 sequence. If the sequence is further apart or closer together, it means that the dna helix made more or less of a full turn, and the holoenzyme can’t bind as efficiently

25
Q

Elongation in e.coli

A

Rna polymerase add s about 40 nucleotides per second. The transcription bubble is 18 nucleotides wide and moves with the rna polymerase. Rna stays base paired with template for 8bp

26
Q

Termination in E.coli

A

Can be either rho dependent or rho independent

27
Q

Rho independent termination

A
  1. Hairpin structure causes the rna polymerase to slow down or pause
  2. An Adenine rich stretch in template strand leads to a Uracil rich stretch in Rna.
  3. This causes weak associations between rna and Dna
  4. Rna polymerase falls off
28
Q

Rho dependent termination

A
  1. Inverted repeats from hairpin slows down/ stop rna polymerase
  2. Upstream from inverted repeats is a stretch of dna that won’t form a secondary structure as rna
  3. Unstructured rna allows rho to bind and once it catches up with rna pol it unwinds rna/dna hybrid
  4. Release of rna
29
Q

Transcription in eukaryotes vs prokaryotes

A

Very similar just a bit more complicated.
Rna polymerase have additional parts

30
Q

What does RNA pol I create

A

Large rRNA (ribosomal RNAs

31
Q

what does RNA pol II create

A

mRNAs
some snRNAs
miRNA precursors

32
Q

what does RNA pol III create

A

5s rRNA
tRNAs
some snRNAs
RNAs

33
Q

what does core RNA polymerase consist of

A

multiple protein subunits, accessory proteins

34
Q

transcription initiation in eukaryotes

A

TBP and TFIID binds to TATA box
TBP recruits RNA pol II and other TF to create PIC
RNA pol II separates from the TFs (they stay at promoter so they can recruit the next polymerase) and starts transcription
CTD of RPB1 subunit is phosphorlated

35
Q

what does rna pol II create

A
36
Q

what does rna pol III create

A
37
Q

Initiation in Eukaryotes (pol II)

A
  • TBP and TFIID bind to TATA box
  • TBP recruits TFs and RNA pol II to create PIC
  • RNA pol II separates from the PIC
  • CTD of RPB1 subunit of RNA pol II is phoshporylated
38
Q

rna pol I promoter

A
  • contains two dna sequences (core element and upstream element)
  • requires two factors (UBF binds to both elements and recruits SL1, SL1 contains TBP and recruits RNA pol 1)
39
Q

rna pol III promoter

A
  • vary in structure (some look like RNA pol II promoters)
  • 5S rRNA and tRNA have internal promoters that bind RNA pol III specific TF
40
Q

termination rna pol I

A
  • uses termination factor which binds to a DNA sequence downstream of termination site
41
Q

termination pol III

A
  • terminates after string of U, no need for hairpin
42
Q

termination pol II

A
  • tends to stop at random places in a region that can stretch several hundred bp
  • likely promoted once mRNA is cleaved and polyA tail is added
43
Q
A

Genetik (13 decks)

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