Dna Transcription Flashcards
information flow in the central dogma
- DNA replication (DNA -> DNA)
- Transcription (DNA -> RNA)
- Translation (RNA -> Protein)
in all living organisms, genetic information flows…
…from DNA to RNA to Proteins in a unidirectional pathway
exceptions to the central dogma
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)
is translation unidirectional
yes, translation has so far proven to be unidirectional
RNA is the essential…
…intermediate between DNA and proteins
RNA primary structure
- four different nucleotides
- each nucleotide contains one base, ribose, phosphate
- joined through phosphodiester bonds
- polarity from 5’ -> to 3’
what are the consequences of the differences in primary structure between RNA and DNA
- T (5-methyl-U) and U both base pair with A
- the presence of 2’ OH makes RNA sugar-phosphate backbone more sensitive to hydrolysis
RNA secondary structure
- very different to DNA
- contains only one strand which makes them very flexible
- RNA molecules can make intramolecular base pairs on the same strands -> creating crazy structures like hairpins, stems etc due to palindromes
base pairing rules in RNA
- same as in DNA meaning Chargaffs rules apply here as well
- A-U, G-C
- The only exception is that G can technically base pair with U; they don’t contribute to stability
stability of stems
depends on
1. length: long > short
2. sequence (number of hydrogen bonds): GC>AU>GU
Palindromes
a word or a phrase that reads the same forwards and backwards
palindromes in DNA sequence
sequences where the same sequence is found not on the same strand, but rather on the complementary strands
complex 3d structures of RNA
- can be stably folded into complex structures
- this freedom allows RNA to develop catalytic abilities -> ribozymes
- RNA catalyses some of the key reactions in RNA processing and translation
transcription definition
synthesis of RNA from a DNA template
RNA transcription requirements
- ssDNA
- activated (triphosphate) nucleotide precursors
- transcription proteins (RNA polymerase)
RNA polymerases
transcription protein in RNA transcription that can start new chains
Biochemistry of polymerization
- free 3’ OH attacks alpha phosphate
- release of pyrophosphate (PPi)
- Hydrolysis of PPi
What is RNA catalyst
Is a ribozyme that catalyzes many key reactions during processing and translation
Transcription in rna vs dna
Transcription is basically the same. However, rna polymerase unwinds dna helix itself, and always the same strand is transcribed for a gene
What is required for transcription
- Different accessory proteins
- Transcription bubble
- Does not require a primer
Transcription in E.coli initiation
- Sigma factor associates with core RNA polymerase
- Holoenzyme binds to promoter
- Sigma factor promotes melting of dna, which generates an open complex
- First nucleotide binds to +1 position, and second one binds as well
- Rna pol catalzys first phosphordiester bond
- Core polymerase escapes from promoter, and only Sigma factor is left behind
Promoter recognition in E.coli
The promoter has a consensus sequence that the holoenzyme binds to. Different sigma factors will recognise different consensus sequences
What determines how well the holoenzyme binds to the promoter
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
Elongation in e.coli
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
Termination in E.coli
Can be either rho dependent or rho independent
Rho independent termination
- Hairpin structure causes the rna polymerase to slow down or pause
- An Adenine rich stretch in template strand leads to a Uracil rich stretch in Rna.
- This causes weak associations between rna and Dna
- Rna polymerase falls off
Rho dependent termination
- Inverted repeats from hairpin slows down/ stop rna polymerase
- Upstream from inverted repeats is a stretch of dna that won’t form a secondary structure as rna
- Unstructured rna allows rho to bind and once it catches up with rna pol it unwinds rna/dna hybrid
- Release of rna
Transcription in eukaryotes vs prokaryotes
Very similar just a bit more complicated.
Rna polymerase have additional parts
What does RNA pol I create
Large rRNA (ribosomal RNAs
what does RNA pol II create
mRNAs
some snRNAs
miRNA precursors
what does RNA pol III create
5s rRNA
tRNAs
some snRNAs
RNAs
what does core RNA polymerase consist of
multiple protein subunits, accessory proteins
transcription initiation in eukaryotes
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
what does rna pol II create
what does rna pol III create
Initiation in Eukaryotes (pol II)
- 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
rna pol I promoter
- 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)
rna pol III promoter
- vary in structure (some look like RNA pol II promoters)
- 5S rRNA and tRNA have internal promoters that bind RNA pol III specific TF
termination rna pol I
- uses termination factor which binds to a DNA sequence downstream of termination site
termination pol III
- terminates after string of U, no need for hairpin
termination pol II
- 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
